Risteys · CD2_BENIGN_LIPO_SPERMATIC

Endpoint definition steps	FinnGen
Phenotype data
1. Apply sex-specific rule only males	-
2. Check conditions None
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.	-
4. Check minimum number of events None	-
5. Include endpoints None	-
6. Filter based on genotype QC (FinnGen only) None	-

Summary Statistics

↥

-FinRegistry-

This endpoint is excluded from FinRegistry analyses (omitted endpoint).

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	48	-	48
Unadjusted period prevalence (%)	0.02	-	0.02
Median age at first event (years)	54.27	-	54.27

-FinnGen-

Age distribution of first events

-FinnGen-

Year distribution of first events

-FinnGen-

Cumulative Incidence Function

Not a core endpoint, no data to show.

CodeWAS (R11)

↥

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.

No data available

LabWAS

↥

(ID) Name

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

4.57

6.15

3.0

2.0

—

(40761535) Cells panel - Urine sediment

6.50

5.83

2.9

3.1

—

(3044640) Blood type and Crossmatch panel - Blood

3.83

4.91

3.2

2.0

—

(3019060) Gas panel - Arterial blood

5.48

4.54

12.9

5.3

—

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

130

3.46

4.29

7.3

3.4

—

(3043409) Potassium [Moles/volume] in Arterial blood

8.86

3.69

11.7

4.4

4.1

4.0

mmol/l

—

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

4.42

3.56

2.8

1.7

—

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

4.25

3.40

2.8

1.6

—

(3011397) Hemoglobin [Presence] in Urine by Test strip

3.16

3.26

5.0

2.4

—

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

3.50

3.22

3.1

1.6

—

(3023368) Bacteria identified in Blood by Culture

2.76

2.75

7.4

3.9

—

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

6.05

2.63

1.8

1.5

—

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

7.80

2.61

1.4

—

(3026008) Bacteria identified in Urine by Culture

2.88

2.50

5.2

3.2

—

(3006217) Methemoglobin/Hemoglobin.total in Arterial blood

4.15

2.49

10.4

11.0

0.7

—

(3028653) Carboxyhemoglobin/Hemoglobin.total in Arterial blood

3.96

2.39

10.4

10.6

1.3

1.9

—

(3022145) Colonoscopy Study observation

3.58

2.37

1.2

—

(3002385) Erythrocyte distribution width [Ratio]

277

0.40

2.31

38.5

16.0

13.7

13.5

0.28

267

(3016251) Hemoglobin.gastrointestinal [Presence] in Stool

3.72

2.05

2.0

—

(3019150) Specific gravity of Urine by Refractometry

2.54

2.00

5.9

2.4

—

1.0

—

(3020779) Urea [Moles/volume] in Serum or Plasma

2.93

1.92

24.6

14.0

9.8

13.3

mmol/l

—

(4035726)

4.16

1.76

1.0

1.4

—

(3006140) Bilirubin.total [Moles/volume] in Serum or Plasma

162

2.13

1.75

7.9

4.5

9.5

12.6

umol/l

1.07

155

(40768797) Stomach Pathology biopsy report

2.67

1.74

1.6

1.1

—

(40760892) CBC W Ordered Manual Differential panel - Blood

2.29

1.56

6.5

4.3

—

(3002256) Pathology report gross observation

2.81

1.25

1.2

1.1

—

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

2.49

1.23

1.2

1.6

—

(40763086) Leukocyte esterase [Presence] in Urine by Automated test strip

124

1.88

1.21

5.5

3.0

—

(3007853) Bacteria identified in Skin by Aerobe culture

2.12

1.10

3.0

2.3

—

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

112

1.80

1.03

2.7

2.1

189.6

292.8

u/l

0.63

104

(3015736) pH of Urine

121

1.78

1.02

5.2

2.7

—

(3037522) Nuclear Ab [Titer] in Serum

2.14

0.90

1.2

1.4

—

338.2

—

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

1.83

0.88

1.7

1.3

—

(40768804) Tissue Pathology biopsy report

1.76

0.87

1.6

1.3

—

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

1.83

0.74

3.9

6.4

—

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

1.87

0.68

4.2

2.9

—

(3009542) Hematocrit [Volume Fraction] of Blood

318

0.65

0.66

25.9

14.1

40.2

41.9

0.24

224

(3013721) Aspartate aminotransferase [Enzymatic activity/volume] in Serum or Plasma

121

0.59

0.66

4.8

2.9

25.5

30.9

u/l

—

112

(1761868) Lipid panel - Serum or Plasma

134

0.60

0.63

2.9

3.1

—

(3016431) Calcium.ionized [Moles/volume] adjusted to pH 7.4 in Serum or Plasma

145

1.51

0.62

23.8

8.2

1.2

mmol/l

0.23

126

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

1.59

0.59

1.6

1.5

15.9

16.7

nmol/l

—

(3018677) aPTT in Platelet poor plasma by Coagulation assay

1.50

0.55

1.3

1.7

27.8

29.3

—

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

1.54

0.49

1.3

1.8

2.4

mmol/l

—

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

105

1.47

0.48

5.4

2.6

367.1

8254.2

umol/l

0.79

(3042936) Bacteria identified in Isolate by Culture

1.54

0.46

2.5

1.8

—

(44816559) Phosphatidylethanol [Mass/volume] in Blood

0.00

0.42

0.0

1.1

—

(3000330) Specific gravity of Urine by Test strip

0.00

0.42

0.0

6.6

—

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

1.43

0.39

4.2

1.4

—

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

119

1.38

0.38

3.0

2.6

—

(3041096) Erythrocytes [Presence] in Urine by Automated

0.63

0.37

4.2

3.1

—

(36304419) Bacteria [Presence] in Urine

1.42

0.36

3.3

2.1

—

(40758558) Short blood count panel - Blood

1.28

0.29

16.9

6.0

—

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

1.31

0.24

4.6

1.7

—

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

1.21

0.22

1.4

1.2

—

25.8

—

(3016879) Cocaine [Presence] in Urine

0.00

0.21

0.0

1.3

—

(3000764) Benzodiazepines [Presence] in Urine

0.00

0.21

0.0

1.3

—

(3027944) Amphetamines [Presence] in Urine

0.00

0.21

0.0

1.3

—

(3028300) Cannabinoids [Presence] in Urine

0.00

0.21

0.0

1.3

—

(3027008) Opiates [Presence] in Urine

0.00

0.21

0.0

1.3

—

(3037756) Immunofixation for Serum or Plasma

0.00

0.21

0.0

1.7

—

(4094501)

0.00

0.21

0.0

1.1

—

(3037121) Protein [Mass/volume] in Urine

0.00

0.21

0.0

4.4

—

0.1

—

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

0.00

0.21

0.0

6.6

—

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

396

1.24

0.16

13.1

8.9

28.7

28.8

u/l

0.00

377

(3044889) 12 lead EKG panel

247

0.87

0.12

4.8

3.9

—

(3013512) EKG study

115

0.84

0.12

5.1

4.5

—

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

1.12

0.10

5.6

1.7

—

(3000494) Fungus identified in Specimen by Culture

1.12

0.10

1.0

1.6

—

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

367

1.17

0.09

4.4

4.8

6.0

6.2

mmol/l

0.22

338

(3035995) Alkaline phosphatase [Enzymatic activity/volume] in Serum or Plasma

267

1.12

0.08

10.9

5.4

68.0

74.8

u/l

1.05

247

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

237

1.11

0.08

3.6

3.4

24.3

24.4

0.02

115

(3020564) Creatinine [Moles/volume] in Serum or Plasma

399

1.19

0.08

28.9

15.4

116.2

91.2

umol/l

0.82

399

(40761511) CBC panel - Blood by Automated count

379

0.90

0.04

21.0

12.0

—

(42870588) Differential panel, method unspecified - Blood

108

0.91

0.03

11.9

6.5

—

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

386

0.93

0.01

32.9

15.7

4.2

4.0

mmol/l

1.21

374

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

185

0.96

0.00

3.6

2.2

—

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

384

0.95

0.00

33.3

15.7

139.6

139.5

mmol/l

0.13

372

(3037467) Urinalysis macro (dipstick) panel - Urine

216

1.03

0.00

7.0

3.8

—

(3021952) Alkaline phosphatase isoenzymes [Enzymatic activity/volume] in Serum or Plasma by Heat stability

0.00

0.0

2.2

—

(3026361) Erythrocytes [#/volume] in Blood

415

1.10

0.00

37.9

18.0

4.6

4.7

e12/l

0.14

399

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

0.00

0.0

1.2

—

(3034770) Mitochondria Ab [Titer] in Serum

0.00

0.0

1.0

—

(3009041) Cardiolipin IgG Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.4

—

7.6

—

(3035941) MCH [Entitic mass]

415

1.10

0.00

37.8

17.8

30.0

30.7

1.48

405

(3006442) Creatine [Moles/volume] in Serum or Plasma

0.00

0.0

1.2

—

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

0.00

0.0

3.0

—

4.3

—

(3011288) Drugs identified in Urine by Screen method

0.00

0.0

1.2

—

(3008364) Apolipoprotein A-I [Mass/volume] in Serum or Plasma

0.00

0.0

1.4

—

(1175715) Chlamydophila pneumoniae IgM Ab [Presence] in Serum by Immunoassay

0.00

0.0

1.2

—

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

0.00

0.0

4.7

—

(3036489) Thrombin time

0.00

0.0

2.2

—

20.7

—

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

0.00

0.0

1.0

—

(3051714) Fibrin D-dimer FEU [Mass/volume] in Platelet poor plasma

0.92

0.00

1.0

1.6

0.3

1.0

mg/l

—

(3000963) Hemoglobin [Mass/volume] in Blood

415

1.10

0.00

38.0

18.1

137.6

142.4

g/l

1.02

405

(3000515) Antithrombin actual/normal in Platelet poor plasma by Chromogenic method

0.00

0.0

2.4

—

85.9

—

(36033641) SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Rapid immunoassay

0.00

0.0

1.0

—

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

0.00

0.0

3.0

—

(3024731) MCV [Entitic volume]

414

1.12

0.00

37.8

18.0

90.5

91.6

0.60

404

(40762485) Glomerular basement membrane Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.0

—

(40760888) Immunoglobulin light chains.free panel - Serum

0.00

0.0

1.1

—

(3014791) Apolipoprotein B [Mass/volume] in Serum or Plasma

0.00

0.0

1.4

—

0.8

—

(3029080) Hemoglobin [Entitic mass] in Reticulocytes

0.00

0.0

1.4

—

35.2

—

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

0.00

0.0

2.3

—

1.0

—

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

0.00

0.0

3.0

—

104.8

—

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

0.00

0.0

1.4

—

(3008757) Leukocyte morphology finding [Identifier] in Blood

0.00

0.0

6.0

—

(3011831) Apolipoprotein B/Apolipoprotein A-I [Percentile]

0.00

0.0

1.4

—

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

0.00

0.0

2.1

—

0.2

—

(4062490)

0.00

0.0

1.0

—

(3052851) Hemolysis interference index of Serum or Plasma

0.00

0.0

4.1

—

Mortality – FinRegistry

↥

This endpoint is excluded from FinRegistry analyses (omitted endpoint).

Relationships between endpoints

↥

Index endpoint: CD2_BENIGN_LIPO_SPERMATIC_EXALLC – Benign lipomatous neoplasm of spermatic cord

GWS hits: -

This endpoint is excluded from FinRegistry analyses (omitted endpoint).

NAME	CD2_BENIGN_LIPO_SPERMATIC_EXALLC
CONTROL_EXCLUDE	C3_CANCER\|C3_CANCER_WIDE
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

≡ Risteys

FG R12 + FR

FinnGen R11 + FinRegistry

FinnGen R10 + FinRegistry

FinnGen R10

FinnGen R9

FinnGen R8

FinnGen R7

FinnGen R6

FinnGen R5

FinnGen R4

FinnGen R3

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)

All original rules

Similar endpoints

Case counts by codes

Summary Statistics

-FinRegistry-

-FinnGen-

Key figures

-FinnGen-

Age distribution of first events

-FinnGen-

Year distribution of first events

-FinnGen-

Cumulative Incidence Function

CodeWAS (R11)

LabWAS

Mortality – FinRegistry

Relationships between endpoints