Benign lipomatous neoplasm of spermatic cord

CD2_BENIGN_LIPO_SPERMATIC

adrenal gland neoplasm: A neoplasm (disease) that involves the adrenal gland.

Endpoint definition

↥

Report an error or suggest an improvement for this endpoint codes

Endpoint definition steps	FinnGen
Phenotype data	557745
1. Apply sex-specific rule only males	244368
2. Check conditions None	244368
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — D17.6& Cause of death: ICD-10 — D17.6& 2 out of 7 registries used, show all original rules.	51
4. Check minimum number of events None	51
5. Include endpoints None	51
6. Filter based on genotype QC (FinnGen only)	50

Control definitions (FinnGen only)

Controls for this endpoint are individuals that are not cases.

Extra metadata

Level in the ICD hierarchy: 3
First used in FinnGen datafreeze: DF2
Parent code in ICD-10: D17
Name in latin: Neoplasma benignum lipomatosum funiculi spermatici

NAME	CD2_BENIGN_LIPO_SPERMATIC
CONTROL_EXCLUDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX	1
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D176
HD_ICD_9	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
HD_ICD_8	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	D176
COD_ICD_9	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
COD_ICD_8	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
COD_ICD_10_EXCL
COD_ICD_9_EXCL
COD_ICD_8_EXCL
OPER_NOM
OPER_HL
OPER_HP1
OPER_HP2
KELA_REIMB
KELA_REIMB_ICD
KELA_ATC_NEEDOTHER
KELA_ATC
KELA_VNRO_NEEDOTHER
KELA_VNRO
CANC_TOPO
CANC_TOPO_EXCL
CANC_MORPH
CANC_MORPH_EXCL
CANC_BEHAV

Similar endpoints

↥

List of similar endpoints to Benign lipomatous neoplasm of spermatic cord based on the number of shared cases.

Similar with more cases:

Similar with less cases:

None

Case counts by codes

↥

FinnGen case counts by registry codes:

Upset plot

Full data table

Summary Statistics

↥

-FinRegistry-

Key figures

	All	Female	Male
Number of individuals
Whole population	543	-	543
Only index persons	497	-	497
Unadjusted period prevalence (%)
Whole population	0.02	-	0.02
Only index persons	0.02	-	0.02
Median age at first event (years)
Whole population	-	-	57.75
Only index persons	-	-	56.61

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	50	-	50
Unadjusted period prevalence (%)	0.02	-	0.02
Median age at first event (years)	55.57	-	55.57

-FinRegistry-

Age distribution of first events

-FinnGen-

Age distribution of first events

-FinRegistry-

Year distribution of first events

-FinnGen-

Year distribution of first events

-FinRegistry-

Cumulative Incidence Function

-FinnGen-

Cumulative Incidence Function

No data

CodeWAS

↥

CodeWAS is a tool for exploring the associations between an endpoint and all of the medical codes and drug codes.

This is a new tool, please reach out using the contact form for feedback and improvement ideas.

First, a cohort is built by matching controls to the endpoint cases using year of birth and sex. Then, a Fisher test is done for all the medical codes and drug codes between the cases and controls of this cohort. Codes are reported in the table below if they have −log₁₀(p-value) ≥ 6.

Matched cohort

Matched cases
50: Matched controls
500

Code

Vocabulary

Description

Odds Ratio

-log₁₀(p)

N matched cases

N matched controls

D17.6

ICD-10 Finland

Benign lipomatous neoplasm of spermatic cord

+∞

71.5

JAB30

NOMESCO Finland

Repair of inguinal hernia using prosthetic material

17.2

23.2

KFW96

NOMESCO Finland

Other operation on scrotum or scrotal organs

+∞

20.1

K40.9

ICD-10 Finland

Unilateral or unspecified inguinal hernia, without obstruction or gangrene

13.9

18.9

LabWAS

↥

N Cases

N Controls

-log₁₀(p)

cases

controls

cases

controls

unit

-log₁₀(p)

N cases

N controls

(46236098) ABO and Rh group [Type] in Blood by Confirmatory method

100

3.14

3.69

3.1

3.4

—

(40761535) Cells panel - Urine sediment

4.92

3.66

2.9

3.7

—

(3019060) Gas panel - Arterial blood

3.90

2.79

12.9

4.6

—

(3044640) Blood type and Crossmatch panel - Blood

134

2.52

2.56

3.3

3.2

—

(3016251) Hemoglobin.gastrointestinal [Presence] in Stool

4.10

2.24

2.0

2.2

—

(3003327) Ova and parasites identified in Stool by Light microscopy

5.41

2.12

1.4

1.2

—

(3001079) Blood group antibody screen [Presence] in Serum or Plasma

186

2.15

1.84

4.7

3.3

—

estimate

—

(3026008) Bacteria identified in Urine by Culture

2.23

1.71

5.3

2.7

—

(3023368) Bacteria identified in Blood by Culture

132

2.02

1.54

6.9

5.1

—

(3038288) Influenza virus B RNA [Presence] in Specimen by NAA with probe detection

2.28

1.40

2.6

1.7

—

(3044938) Influenza virus A RNA [Presence] in Specimen by NAA with probe detection

2.10

1.38

2.9

1.9

—

(3024950) Chlamydia trachomatis DNA [Presence] in Urine by NAA with probe detection

2.81

1.24

3.0

1.8

—

(3043924) Respiratory syncytial virus RNA [Identifier] in Specimen by NAA with probe detection

2.15

1.23

2.6

1.6

—

(586526) SARS-CoV-2 (COVID-19) RNA [Presence] in Nasopharynx by NAA with probe detection

2.48

1.22

1.2

1.5

—

(1761868) Lipid panel - Serum or Plasma

171

0.48

1.22

3.2

3.4

—

(3022145) Colonoscopy Study observation

2.16

1.11

1.4

1.3

—

(44816559) Phosphatidylethanol [Mass/volume] in Blood

0.00

1.01

0.0

1.5

—

0.48

—

(3007853) Bacteria identified in Skin by Aerobe culture

2.02

1.00

2.8

2.0

—

(3014576) Chloride [Moles/volume] in Serum or Plasma

1.91

0.99

12.1

8.7

104.58

103.63

mmol/l

0.44

(3037522) Nuclear Ab [Titer] in Serum

2.02

0.93

1.1

1.4

—

360.00

—

(40768797) Stomach Pathology biopsy report

1.94

0.91

1.8

1.2

—

(3051552) Clostridioides difficile toxin genes [Presence] in Stool by NAA with probe detection

2.06

0.87

1.8

—

(3013115) Eosinophils [#/volume] in Blood

222

1.59

0.81

9.1

7.5

0.19

0.20

e9/l

0.14

196

(3020891) Body temperature

2.02

0.73

2.8

4.7

36.52

36.98

°c

—

(3001604) Monocytes [#/volume] in Blood

216

1.54

0.73

7.2

7.4

0.60

0.64

e9/l

0.26

185

(3006315) Basophils [#/volume] in Blood

217

1.53

0.70

7.2

7.4

0.03

0.04

e9/l

0.39

189

(3036481) Cortisol [Moles/volume] in Serum or Plasma

1.73

0.70

1.9

306.71

393.26

nmol/l

—

(3019198) Lymphocytes [#/volume] in Blood

218

1.52

0.68

7.7

2.01

1.70

e9/l

1.01

193

(3003785) Carcinoembryonic Ag [Mass/volume] in Serum or Plasma

1.71

0.65

3.9

5.0

3.33

7.53

ug/l

—

(3007778) Kappa light chains/Lambda light chains [Mass Ratio] in Serum

0.00

0.61

0.0

2.8

—

1.36

—

(3048689) Calprotectin [Mass/mass] in Stool

1.81

0.60

1.3

2.0

155.33

144.29

ug/g

—

(40760892) CBC W Ordered Manual Differential panel - Blood

101

1.54

0.57

6.2

5.7

—

(3018677) aPTT in Platelet poor plasma by Coagulation assay

1.60

0.56

1.3

2.3

28.16

29.25

0.31

(3015736) pH of Urine

176

1.45

0.55

5.6

3.2

6.47

6.16

0.88

101

(3014051) Protein [Presence] in Urine by Test strip

116

0.63

0.54

4.5

2.7

—

0.40

—

(3045783) Sodium and Potassium panel [Moles/volume] - Serum or Plasma

1.50

0.48

3.9

8.7

—

(3017446) Testosterone [Moles/volume] in Serum or Plasma

0.61

0.48

3.3

2.5

11.03

13.71

nmol/l

—

(3044889) 12 lead EKG panel

299

0.73

0.45

5.0

4.8

—

(3022313) Gas panel - Capillary blood

1.52

0.41

2.6

3.6

—

(3042936) Bacteria identified in Isolate by Culture

1.42

0.41

2.7

2.1

—

(3045414) Leukocytes [Presence] in Urine

1.45

0.36

1.7

2.0

—

0.00

estimate

—

(3017143) Hepatitis C virus Ab [Presence] in Serum

1.45

0.36

4.5

2.1

—

(3007220) Creatine kinase [Enzymatic activity/volume] in Serum or Plasma

139

1.34

0.35

2.8

2.2

189.59

330.05

u/l

0.48

130

(3005772) Bilirubin.conjugated [Moles/volume] in Serum or Plasma

1.35

0.34

11.3

3.6

5.23

6.36

umol/l

—

(43054903) Holo-transcobalamin II [Moles/volume] in Serum

179

1.30

0.32

2.1

2.0

83.16

92.02

pmol/l

0.32

(3023103) Potassium [Moles/volume] in Serum or Plasma

427

0.78

0.27

35.7

21.5

4.15

4.03

mmol/l

1.54

419

(3019550) Sodium [Moles/volume] in Serum or Plasma

425

0.80

0.27

35.9

21.6

139.59

139.42

mmol/l

0.20

419

(3004588) Protein electrophoresis panel - Serum or Plasma

1.35

0.24

1.4

3.1

—

(40758558) Short blood count panel - Blood

114

0.74

0.23

15.2

7.1

—

(3004809) Band form neutrophils/Leukocytes in Blood

0.00

0.21

0.0

4.2

—

0.55

—

(21494670) JAK2 gene exon 14 targeted mutation analysis in Blood or Tissue by Molecular genetics method

0.00

0.21

0.0

1.1

—

(3027544) Mycobacterium sp identified in Sputum by Organism specific culture

0.00

0.21

0.0

2.8

—

(3019284) Hepatitis B virus surface Ag [Presence] in Serum

1.31

0.21

4.0

1.8

—

(3029080) Hemoglobin [Entitic mass] in Reticulocytes

0.00

0.21

0.0

3.2

—

32.67

—

(3016879) Cocaine [Presence] in Urine

0.00

0.21

0.0

1.2

—

(3000764) Benzodiazepines [Presence] in Urine

0.00

0.21

0.0

1.2

—

(3028300) Cannabinoids [Presence] in Urine

0.00

0.21

0.0

1.2

—

(3000620) Complement C3 [Mass/volume] in Serum or Plasma

0.00

0.21

0.0

1.5

—

1.28

—

(3027008) Opiates [Presence] in Urine

0.00

0.21

0.0

1.2

—

(3027944) Amphetamines [Presence] in Urine

0.00

0.21

0.0

1.2

—

(3017766) Complement C4 [Mass/volume] in Serum or Plasma

0.00

0.21

0.0

1.3

—

0.26

—

(3003694) ABO and Rh group [Type] in Blood

109

1.26

0.21

1.6

1.4

—

(3021387) Prolactin [Units/volume] in Serum or Plasma

0.00

0.21

0.0

1.3

—

301.00

—

(3000012) Reticulocyte production index

0.00

0.21

0.0

3.0

—

0.96

—

(3017044) Thyrotropin receptor Ab [Units/volume] in Serum

0.00

0.21

0.0

2.5

—

5.42

—

(4094501) Cardiovascular stress test using bicycle ergometer

0.00

0.21

0.0

1.2

—

(1761482) Bacteria [#/volume] in Urine by Culture

0.00

0.20

0.0

5.0

—

(3037756) Immunofixation for Serum or Plasma

0.00

0.20

0.0

1.3

—

(40760888) Immunoglobulin light chains.free panel - Serum

0.00

0.20

0.0

5.6

—

(40768804) Tissue Pathology biopsy report

161

0.82

0.18

1.8

2.1

—

(46235355) HIV 1 and 2 tests - Meaningful Use set

1.15

0.18

4.9

1.8

—

(3015377) Calcium [Moles/volume] in Serum or Plasma

140

0.81

0.18

15.8

3.5

2.37

2.32

mmol/l

0.70

122

(3026493) Urate [Moles/volume] in Serum or Plasma

140

1.21

0.18

5.5

3.5

373.19

372.38

umol/l

0.01

120

(3021337) Troponin I.cardiac [Mass/volume] in Serum or Plasma

0.74

0.17

7.7

4.3

73.83

445.79

ng/l

—

(3019800) Troponin T.cardiac [Mass/volume] in Serum or Plasma

201

1.17

0.15

3.7

4.3

41.00

49.83

ng/l

0.20

158

(42870588) Differential panel, method unspecified - Blood

144

1.16

0.12

8.8

7.2

—

(3021960) Folate [Moles/volume] in Serum or Plasma

135

1.16

0.11

1.9

1.7

16.25

18.10

nmol/l

—

109

(21494755) Public health laboratory ask at order entry panel

1.18

0.10

2.0

1.3

—

(4035726) Immunohistochemistry procedure

1.12

0.10

1.0

1.4

—

(3019902) Methicillin resistant Staphylococcus aureus [Presence] in Specimen by Organism specific culture

1.15

0.09

4.0

3.9

—

(3026361) Erythrocytes [#/volume] in Blood

444

0.93

0.09

41.3

27.5

4.60

4.57

e12/l

0.12

433

(3013512) EKG study

173

0.89

0.08

4.1

4.2

—

(40761511) CBC panel - Blood by Automated count

418

0.89

0.07

21.3

17.4

—

(3013826) Glucose [Moles/volume] in Serum or Plasma

278

1.10

0.07

11.9

5.6

6.29

6.82

mmol/l

1.63

267

(3018251) Fasting glucose [Moles/volume] in Serum or Plasma

400

0.89

0.06

5.4

5.9

6.07

6.15

mmol/l

0.11

368

(3001784) Prostate Specific Ag Free/Prostate specific Ag.total in Serum or Plasma

271

0.92

0.05

4.6

4.8

24.42

21.57

0.72

142

(3029287) Urinalysis microscopic panel [#/volume] - Urine by Automated count

171

0.99

0.00

3.1

—

(3043362) Influenza virus B Ag [Presence] in Nasopharynx by Immunoassay

0.00

0.0

1.2

—

(3009466) Valproate [Moles/volume] in Serum or Plasma

0.00

0.0

5.3

—

347.50

—

(3046524) Influenza virus A Ag [Presence] in Nasopharynx by Immunoassay

0.00

0.0

1.2

—

(3049539) Genetic diseases [Identifier] in Blood or Tissue by FISH Nominal

0.00

0.0

1.5

—

(3025468) Yersinia sp identified in Specimen by Organism specific culture

0.00

0.0

2.8

—

(3006923) Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma

432

0.97

0.00

15.5

13.2

28.16

28.74

u/l

0.10

420

(40760847) Basement membrane Ab [Titer] in Serum by Immunofluorescence

0.00

0.0

1.2

—

(3012568) Campylobacter sp identified in Specimen by Organism specific culture

0.00

0.0

2.8

—

(43055361) Metamyelocytes/Leukocytes [Pure number fraction] in Blood by Manual count

0.00

0.0

1.8

—

1.50

—

(3024522) Salmonella sp identified in Specimen by Organism specific culture

0.00

0.0

2.8

—

(3052649) Adenosine deaminase [Enzymatic activity/volume] in Serum or Plasma

0.00

0.0

1.5

—

14.17

—

(3035637) Corticotropin [Mass/volume] in Plasma

0.00

0.0

1.2

—

17.50

—

(42868716) Shigella species+EIEC invasion plasmid antigen H ipaH gene [Presence] in Stool by NAA with probe detection

0.00

0.0

2.8

—

(40757349) CD3+CD4+ (T4 helper) cells/CD3+CD8+ (T8 suppressor cells) cells [# Ratio] in Blood

0.00

0.0

1.7

—

1.61

—

(3021125) Hepatitis C virus RNA [Presence] in Serum or Plasma by NAA with probe detection

0.00

0.0

1.7

—

(40759850) Jo-1 extractable nuclear Ab [Presence] in Serum by Immunoblot

0.00

-0.00

0.0

1.2

—

(3035320) C reactive protein [Mass/volume] in Body fluid

0.00

-0.00

0.0

1.8

—

34.40

—

(3000494) Fungus identified in Specimen by Culture

1.04

-0.00

1.0

1.6

—

(3004451) EKG impression Narrative

0.00

-0.00

0.0

1.4

—

(3040359) Human coronavirus NL63 RNA [Presence] in Specimen by NAA with probe detection

0.00

-0.00

0.0

3.3

—

(3041642) Human coronavirus 229E RNA [Presence] in Specimen by NAA with probe detection

0.00

-0.00

0.0

3.3

—

(3038546) Human coronavirus OC43 RNA [Presence] in Specimen by NAA with probe detection

0.00

-0.00

0.0

3.3

—

(3009595) Pneumocystis jirovecii DNA [Presence] in Specimen by NAA with probe detection

0.00

-0.00

0.0

1.6

—

(1001926) Buprenorphine [Presence] in Urine by Screen method

0.00

-0.00

0.0

1.3

—

(37021247) Adenovirus 40+41 DNA [Presence] in Stool by NAA with probe detection

0.00

-0.00

0.0

1.7

—

(3021614) Rheumatoid factor [Units/volume] in Serum or Plasma

1.04

-0.00

1.3

1.2

—

29.06

—

(37020957) Sapovirus genogroups I+II+IV+V RNA [Presence] in Stool by NAA with probe detection

0.00

-0.00

0.0

1.8

—

(3032700) Glomerular basement membrane Ab [Units/volume] in Serum

0.00

-0.00

0.0

1.0

—

(40768795) Lymph node Pathology biopsy report

0.00

-0.00

0.0

1.4

—

(3011288) Drugs identified in Urine by Screen method Nominal

0.00

-0.00

0.0

1.1

—

(3035285) Chloride [Moles/volume] in Venous blood

0.00

-0.00

0.0

4.1

—

105.38

—

(3041354) Potassium [Moles/volume] in Venous blood

0.00

-0.00

0.0

4.1

—

4.16

—

(40768806) Pleura Pathology biopsy report

0.00

-0.00

0.0

1.9

—

(40760848) Basement membrane zone BP180 Ab [Units/volume] in Serum by Immunoassay

0.00

-0.00

0.0

1.2

—

(3045716) Anion gap in Serum or Plasma by calculation

0.00

-0.00

0.0

3.2

—

11.44

—

(3020059) Calcium [Moles/volume] corrected for albumin in Serum or Plasma

0.95

-0.00

3.3

2.9

2.43

2.45

mmol/l

—

(43055089) Myosin Ab [Presence] in Serum or Plasma by Immunoblot

0.00

-0.00

0.0

1.0

—

(40765096) Chromosome analysis panel by Banding

0.00

-0.00

0.0

1.8

—

(3010566) Parathyrin.intact [Moles/volume] in Serum or Plasma

0.00

-0.00

0.0

4.2

—

17.89

—

(706163) SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory system specimen by NAA with probe detection

210

1.00

-0.00

3.3

2.6

—

(3018301) Testosterone Free [Moles/volume] in Serum or Plasma

0.00

-0.00

0.0

1.0

—

176.30

—

(21493466) Plesiomonas shigelloides DNA [Presence] in Stool by NAA with non-probe detection

0.00

-0.00

0.0

2.6

—

(37020445) Astrovirus RNA [Presence] in Stool by NAA with probe detection

0.00

-0.00

0.0

1.7

—

(3002256) Pathology report gross observation

1.04

-0.00

1.3

1.2

—

(3005988) Vibrio sp identified in Specimen by Organism specific culture

0.00

-0.00

0.0

2.6

—

(3044927) Protein electrophoresis panel - Urine

0.00

-0.00

0.0

1.4

—

(3033705) Calcium.ionized [Moles/volume] in Venous blood

0.00

-0.00

0.0

4.1

—

1.19

—

(3034770) Mitochondria Ab [Titer] in Serum

0.00

-0.00

0.0

1.5

—

(3017704) Immunofixation for Urine

0.00

-0.00

0.0

1.0

—

(42869457) Rotavirus RNA [Identifier] in Stool by NAA with probe detection

0.00

-0.00

0.0

1.7

—

(4062490) Immunoglobulin typing, IgG

0.00

-0.00

0.0

1.0

—

(3015816) F5 gene p.Arg506Gln [Presence] in Blood or Tissue by Molecular genetics method

0.00

-0.00

0.0

1.2

—

(3017354) Segmented neutrophils/Leukocytes in Blood

0.00

-0.00

0.0

4.7

—

59.67

—

(3008757) Leukocyte morphology finding [Identifier] in Blood

0.00

-0.00

0.0

5.1

—

Mortality – FinRegistry

↥

Association

Association between endpoint CD2_BENIGN_LIPO_SPERMATIC and mortality.

Females

No data

Males

Parameter	HR [95% CI]	p-value
CD2_BENIGN_LIPO_SPERMATIC	0.961 [0.81, 1.14]	0.64
Birth year	0.985 [0.98, 1.0]	0.003

During the follow-up period (1.1.1998 — 31.12.2019), 145 out of 504 males with CD2_BENIGN_LIPO_SPERMATIC died.

Mortality risk

Mortality risk for people of age

years, who have CD2_BENIGN_LIPO_SPERMATIC.

N-year risk	Females	Males
1	No data	0.174%
5	No data	1.045%
10	No data	2.736%
15	No data	4.963%
20	No data	8.282%

Relationships between endpoints

↥

Index endpoint: CD2_BENIGN_LIPO_SPERMATIC – Benign lipomatous neoplasm of spermatic cord

GWS hits: -

Endpoint

Case Overlap

Survival Analysis

Genetic Correlations

Genetic Signals

N (Jaccard index)

HR [CI]

rg [CI]

Hits

Coloc Hits

FinRegistry

FinnGen

FinRegistry

FinnGen

Loading data

Benign lipomatous neoplasm of spermatic cord

Endpoint definition

Endpoint definition steps

FinnGen

Phenotype data

1. Apply sex-specific rule

2. Check conditions

3. Check pre-conditions, main-only, mode, registry filters

4. Check minimum number of events

5. Include endpoints

6. Filter based on genotype QC (FinnGen only)

Similar endpoints

Case counts by codes

Summary Statistics

-FinRegistry-

Key figures

-FinnGen-

Key figures

-FinRegistry-

Age distribution of first events

-FinnGen-

Age distribution of first events

-FinRegistry-

Year distribution of first events

-FinnGen-

Year distribution of first events

-FinRegistry-

Cumulative Incidence Function

-FinnGen-

Cumulative Incidence Function

CodeWAS

Matched cohort

LabWAS

Mortality – FinRegistry

Association

Females

Males

Mortality risk

Relationships between endpoints