Congenital malformation syndromes due to known exogenous causes, not elsewhere classified

Q17_CONGEN_MALFO_SYNDR_KNOWN_EXOGE_CAUSES_NOT_ELSEW_CLASSIFIED

No definition available.

Endpoint definition

↥

Endpoint definition steps	FinnGen
Phenotype data	520210
1. Apply sex-specific rule None	520210
2. Check conditions None	520210
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — Q86 Cause of death: ICD-10 — Q86 2 out of 7 registries used, show all original rules.	45
4. Check minimum number of events None	45
5. Include endpoints None	45
6. Filter based on genotype QC (FinnGen only)	45

Control definitions (FinnGen only)

Control exclude: Q17_OTHER_CONGEN_MALFO

Extra metadata

Level in the ICD hierarchy: 3
First used in FinnGen datafreeze: DF4
Parent code in ICD-10: Q8
Name in latin: Syndromata malformationum congenitarum e causis externis notis non alibi classificata

NAME	Q17_CONGEN_MALFO_SYNDR_KNOWN_EXOGE_CAUSES_NOT_ELSEW_CLASSIFIED
CONTROL_EXCLUDE	Q17_OTHER_CONGEN_MALFO
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	Q86
HD_ICD_9
HD_ICD_8
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	Q86
COD_ICD_9
COD_ICD_8
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 Congenital malformation syndromes due to known exogenous causes, not elsewhere classified based on the number of shared cases.

Similar with more cases:

Similar with less cases:

Fetal alcohol syndrome (dysmorphic)

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	1153	503	650
Only index persons	998	447	551
Unadjusted period prevalence (%)
Whole population	0.02	0.01	0.02
Only index persons	0.02	0.02	0.02
Median age at first event (years)
Whole population	-	6.49	7.16
Only index persons	7.22	6.84	7.54

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	45	24	21
Unadjusted period prevalence (%)	0.01	0.01	0.01
Median age at first event (years)	17.06	12.36	22.44

-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

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

(3030306) Epithelial cells.non-squamous [#/volume] in Urine by Automated count

6.83

8.56

3.4

2.1

0.6

1.3

e6/l

—

(3029879) Epithelial cells.squamous [#/volume] in Urine by Automated count

5.50

6.36

3.8

2.1

4.4

7.3

e6/l

—

(3030467) Casts [#/volume] in Urine by Automated count

4.63

5.99

4.2

2.3

0.2

0.3

e6/l

0.14

(3042936) Bacteria identified in Isolate by Culture

5.28

4.98

2.2

1.6

—

(3023368) Bacteria identified in Blood by Culture

3.96

4.26

6.8

3.5

—

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

134

3.54

4.12

9.4

5.1

9.7

11.3

umol/l

0.47

125

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

3.39

3.87

8.4

2.7

—

(36304419) Bacteria [Presence] in Urine

3.18

3.28

3.1

2.3

—

(3000991) Gas panel - Venous blood

4.23

2.75

21.9

3.2

—

(3024354) Oxygen [Partial pressure] in Venous blood

4.23

2.75

7.7

2.0

5.5

5.6

kpa

—

(3000850) Epithelial cells [#/volume] in Urine

3.02

2.75

2.9

2.0

9.6

7.2

e6/l

0.28

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

6.10

2.63

4.2

2.7

—

(3007628) Bicarbonate [Moles/volume] standard in Venous blood

4.40

2.60

3.0

2.1

26.7

23.7

mmol/l

—

(3012544) pH of Venous blood

3.75

2.47

8.7

2.5

—

(40761535) Cells panel - Urine sediment

4.67

2.47

7.0

3.2

—

(3000330) Specific gravity of Urine by Test strip

6.85

2.43

10.8

1.8

—

(40758558) Short blood count panel - Blood

2.63

2.38

10.6

6.3

—

(3022313) Gas panel - Capillary blood

4.40

2.36

4.1

8.7

—

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

3.94

2.15

1.7

—

(3013650) Neutrophils [#/volume] in Blood by Automated count

210

2.53

2.14

11.9

7.2

4.4

3.6

e9/l

1.20

185

(36031861) Influenza virus A and B and SARS-CoV-2 (COVID-19) and Respiratory syncytial virus RNA panel - Respiratory system specimen by NAA with probe detection

5.47

2.13

1.6

1.4

—

(3014007) Fractional oxyhemoglobin in Arterial blood

5.47

2.13

37.4

3.8

94.4

94.5

—

(3002032) Base excess in Venous blood by calculation

3.37

2.05

9.6

2.4

3.7

1.5

mmol/l

—

(3033658) Prothrombin time (PT) actual/Normal

2.58

2.02

4.9

2.3

84.9

96.3

1.54

(3016293) Bicarbonate [Moles/volume] in Serum or Plasma

4.15

2.01

13.8

5.6

23.0

23.9

mmol/l

—

(3032080) INR in Blood by Coagulation assay

2.46

1.92

28.3

4.2

1.6

1.1

inr

—

(3001604) Monocytes [#/volume] in Blood

178

2.29

1.90

8.2

5.3

0.6

0.5

e9/l

0.69

164

(3006315) Basophils [#/volume] in Blood

179

2.27

1.86

8.2

5.2

0.0

e9/l

1.18

164

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

3.68

1.81

2.7

1.1

—

(42870588) Differential panel, method unspecified - Blood

111

2.23

1.75

7.8

5.1

—

(3013512) EKG study

2.46

1.67

2.9

2.6

—

(3021589) Normoblasts [#/volume] in Blood

166

2.14

1.66

10.8

6.2

0.0

e9/l

0.00

135

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

2.99

1.66

2.9

2.2

449.6

422.3

nmol/l

—

(3022621) pH of Urine by Test strip

3.30

1.64

2.8

1.9

—

(3013115) Eosinophils [#/volume] in Blood

187

2.11

1.58

9.1

5.2

0.2

e9/l

0.50

171

(3019198) Lymphocytes [#/volume] in Blood

187

2.11

1.58

8.2

5.1

1.9

2.1

e9/l

0.40

173

(3025941) Bacteria identified in Stool by Culture

3.13

1.56

1.5

1.2

—

(40768804) Tissue Pathology biopsy report

116

0.36

1.54

1.8

1.9

—

(3021879) Hepatitis B virus core Ab [Presence] in Serum

2.63

1.54

1.2

1.7

—

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

2.67

1.46

2.3

1.2

—

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

2.67

1.46

2.4

1.4

—

(3002109) Cholesterol in LDL/Cholesterol in HDL [Mass Ratio] in Serum or Plasma

0.00

1.42

0.0

1.5

—

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

2.39

1.40

2.5

1.8

—

(40764999) Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (CKD-EPI)

301

2.29

1.37

20.1

8.2

98.4

98.2

ml/min/173m2

0.01

229

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

2.99

1.32

48.6

4.8

91.6

104.4

mmol/l

—

(3037467) Urinalysis macro (dipstick) panel - Urine

226

1.98

1.29

7.3

4.0

—

(3005719) IgG [Mass/volume] in Serum or Plasma

2.61

1.29

1.8

2.3

9.8

10.1

g/l

—

(3026008) Bacteria identified in Urine by Culture

2.00

1.24

4.7

2.7

—

(3044491) Cholesterol non HDL [Mass/volume] in Serum or Plasma

0.00

1.22

0.0

1.3

—

(3028707) Methadone [Presence] in Urine by Screen method

2.68

1.18

1.4

1.5

—

(3003031) Transferrin.carbohydrate deficient.disialo/Transferrin.total in Serum or Plasma

2.04

1.14

2.3

1.5

1.3

0.56

(3016771) Amylase [Enzymatic activity/volume] in Serum or Plasma

1.91

1.02

3.7

2.4

49.0

55.5

u/l

0.89

(3044640) Blood type and Crossmatch panel - Blood

1.86

0.99

3.9

1.8

—

(3000494) Fungus identified in Specimen by Culture

2.40

0.98

1.2

1.5

—

(3044889) 12 lead EKG panel

179

1.73

0.96

2.4

2.7

—

(3013707) Erythrocyte sedimentation rate by Westergren method

240

1.75

0.92

3.1

3.8

11.5

8.2

mm/h

0.41

224

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

137

1.67

0.84

1.8

2.3

—

(3002256) Pathology report gross observation

0.00

0.82

0.0

1.4

—

(3023421) Hepatitis B virus surface Ab [Units/volume] in Serum

0.00

0.82

0.0

1.7

—

286.9

—

(3022250) Lactate dehydrogenase [Enzymatic activity/volume] in Serum or Plasma by Lactate to pyruvate reaction

2.21

0.77

8.0

4.3

244.0

211.4

u/l

—

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

1.79

0.77

5.9

3.1

—

(3007853) Bacteria identified in Skin by Aerobe culture

1.94

0.77

1.4

1.3

—

(3009508) Creatinine [Moles/volume] in Urine

1.69

0.76

6.4

2.8

8.4

8.8

mmol/l

0.08

(1761868) Lipid panel - Serum or Plasma

120

0.60

0.67

3.5

1.9

—

(43534045) MCM6 gene c.-13910C>T and -13915T>G [Identifier] in Blood or Tissue by Molecular genetics method Nominal

1.81

0.66

1.0

—

(3002385) Erythrocyte distribution width [Ratio]

318

1.66

0.65

24.0

9.6

13.5

13.2

0.56

311

(40763571) Iron/Transferrin [Ratio] in Serum or Plasma

1.75

0.63

2.6

2.0

22.4

28.0

—

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

0.00

0.62

0.0

1.3

—

(43054914) Glucose tolerance 2 hours panel - Serum or Plasma

1.77

0.59

1.5

2.3

—

(3011288) Drugs identified in Urine by Screen method

1.67

0.57

2.0

1.6

—

(40768797) Stomach Pathology biopsy report

1.62

0.55

1.3

1.2

—

(3015736) pH of Urine

131

1.48

0.53

7.1

2.6

—

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

1.57

0.51

1.7

—

(3021601) Nitrite [Presence] in Urine by Test strip

160

1.45

0.51

9.8

4.1

0.0

estimate

—

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

1.58

0.49

3.8

1.8

—

(3007164) IgA [Mass/volume] in Serum or Plasma

105

1.48

0.49

1.4

2.0

g/l

—

(40761536) Microorganisms panel - Urine sediment

1.69

0.45

3.0

—

(3000924) Streptococcus pyogenes [Presence] in Throat by Organism specific culture

0.00

0.42

0.0

1.5

—

(3009261) Glucose [Presence] in Urine by Test strip

165

1.38

0.41

7.0

3.0

0.0

estimate

—

(3017895) Helicobacter pylori Ab [Units/volume] in Serum

0.00

0.41

0.0

1.6

—

(3001122) Ferritin [Mass/volume] in Serum or Plasma

146

1.39

0.41

2.5

2.6

42.4

59.6

ug/l

0.73

139

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

328

0.74

0.32

3.3

3.8

—

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

122

1.34

0.32

1.6

1.7

—

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

152

1.31

0.30

9.3

3.7

—

(3024135) Streptococcus.beta-hemolytic [Presence] in Throat by Organism specific culture

114

1.33

0.30

1.7

—

(3035350) Ketones [Presence] in Urine by Test strip

164

1.27

0.26

7.1

2.9

0.0

estimate

—

(36660697) Celiac disease serology panel - Serum

1.35

0.24

1.0

—

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

1.25

0.23

1.6

1.2

—

(3027545) Mycoplasma pneumoniae Ab [Presence] in Serum by Immunoassay

0.00

0.21

0.0

1.5

—

(3004248) Sex hormone binding globulin [Moles/volume] in Serum or Plasma

0.00

0.21

0.0

1.3

—

32.0

—

(3004588) Protein electrophoresis panel - Serum or Plasma

0.00

0.21

0.0

7.8

—

(3047007) Chlamydophila sp Ab [Presence] in Serum

0.00

0.21

0.0

1.4

—

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

0.00

0.21

0.0

1.3

—

(3016879) Cocaine [Presence] in Urine

1.32

0.21

1.5

1.3

—

(3001308) Cholesterol in LDL [Moles/volume] in Serum or Plasma

308

1.27

0.21

5.0

3.4

2.7

2.8

mmol/l

0.27

285

(3000764) Benzodiazepines [Presence] in Urine

1.18

0.20

1.5

1.3

—

(3028300) Cannabinoids [Presence] in Urine

1.18

0.20

1.5

1.3

—

(3027944) Amphetamines [Presence] in Urine

1.18

0.20

1.5

1.3

—

(3027008) Opiates [Presence] in Urine

1.18

0.20

1.5

1.3

—

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

130

1.23

0.19

8.4

2.9

—

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

1.17

0.18

1.3

1.4

1.9

0.6

mg/l

—

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

114

1.20

0.14

2.1

1.9

—

(3011371) Neisseria gonorrhoeae DNA [Presence] in Specimen by NAA with probe detection

0.81

0.09

3.2

1.8

—

(3048689) Calprotectin [Mass/mass] in Stool

0.77

0.09

2.4

2.7

131.5

111.0

ug/g

—

(40761511) CBC panel - Blood by Automated count

378

1.24

0.08

26.2

7.7

—

(3033319) Streptococcus pyogenes Ag [Presence] in Throat

0.79

0.08

1.2

1.7

—

(3041096) Erythrocytes [Presence] in Urine by Automated

100

1.13

0.06

6.7

2.7

—

(3009542) Hematocrit [Volume Fraction] of Blood

347

1.04

0.00

22.1

8.7

37.8

41.2

0.93

296

(3003510) Neisseria gonorrhoeae DNA [Presence] in Urine by NAA with probe detection

117

1.03

0.00

2.3

—

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

123

0.97

0.00

2.6

2.7

—

(3019832) Treponema pallidum Ab [Presence] in Serum

105

1.06

0.00

1.4

1.7

—

(40760892) CBC W Ordered Manual Differential panel - Blood

0.94

0.00

9.6

5.8

—

(3021236) Streptolysin O Ab [Units/volume] in Serum or Plasma

0.00

0.0

1.2

—

118.9

—

(3006093) Chlamydia trachomatis DNA [Presence] in Specimen by NAA with probe detection

0.97

0.00

2.6

2.0

—

(3042596) Human coronavirus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.0

—

(3023150) Myeloperoxidase Ab [Units/volume] in Serum

0.00

0.0

1.0

—

(3018006) Microscopic observation [Identifier] in Cervix by Cyto stain.thin prep

0.92

0.00

1.5

—

(3030408) 3-Methoxytyramine [Moles/volume] in Serum or Plasma

0.00

0.0

1.4

—

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

0.00

0.0

1.0

—

(40766800) Mycobacterium tuberculosis stimulated gamma interferon release by CD4+ T-cells [Units/volume] corrected for background in Blood

0.00

0.0

1.8

—

(3035797) Protein.monoclonal band 2 [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

6.6

—

0.0

—

(3043453) Neutrophil cytoplasmic Ab.perinuclear [Titer] in Serum

0.00

0.0

1.4

—

(3023465) Gamma globulin [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

6.6

—

7.7

—

(3029713) Protein.monoclonal band 1 [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

6.6

—

2.0

—

(3005082) Progesterone [Moles/volume] in Serum or Plasma

0.00

0.0

1.0

—

29.6

—

(3043723) Beta 1 globulin [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

6.6

—

(3038177) Helicobacter pylori Ab [Presence] in Serum

0.00

0.0

1.0

—

(3023420) DNA double strand Ab [Units/volume] in Serum

0.00

0.0

1.6

—

(3043747) Beta 2 globulin [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

6.6

—

3.1

—

(3037756) Immunofixation for Serum or Plasma

0.00

0.0

1.8

—

(3029338) Protein.monoclonal band 3 [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

6.6

—

0.0

—

(3005229) Alpha 2 globulin [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

6.6

—

6.4

—

(3050380) Cytology report of Cervical or vaginal smear or scraping Cyto stain

0.00

0.0

1.4

—

(3029379) Protein.monoclonal band 4 [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

6.6

—

0.0

—

(40765089) Chromosome analysis panel - Blood by G-banded

0.00

0.0

1.0

—

(3025130) Human papilloma virus identified in Specimen

0.00

0.0

1.7

—

(3015322) Alpha 1 globulin [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

6.6

—

2.7

—

(3008909) Norovirus RNA [Presence] in Stool by NAA with probe detection

0.00

0.0

1.2

—

(3015183) Erythrocyte sedimentation rate

0.00

0.0

1.0

—

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

0.00

0.0

1.1

—

(3047181) Lactate [Moles/volume] in Blood

0.00

0.0

4.2

—

1.1

—

(3042975) Streptococcus sp identified in Isolate by Organism specific culture

0.00

0.0

1.0

—

(40768793) Breast Pathology biopsy report

0.00

0.0

1.1

—

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

0.00

0.0

1.1

—

(3003265) Liver kidney microsomal Ab [Titer] in Serum by Immunofluorescence

0.00

0.0

1.8

—

(3046294) Neutrophil cytoplasmic Ab.classic [Titer] in Serum

0.00

0.0

1.4

—

(3049717) Cytology report of Urine Cyto stain

0.00

0.0

1.6

—

(3028286) Albumin [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.0

6.6

—

38.9

—

Mortality – FinRegistry

↥

Association

Association between endpoint Q17_CONGEN_MALFO_SYNDR_KNOWN_EXOGE_CAUSES_NOT_ELSEW_CLASSIFIED and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have Q17_CONGEN_MALFO_SYNDR_KNOWN_EXOGE_CAUSES_NOT_ELSEW_CLASSIFIED.

N-year risk	Females	Males
1	No data	No data
5	No data	No data
10	No data	No data
15	No data	No data
20	No data	No data

Relationships between endpoints

↥

Index endpoint: Q17_CONGEN_MALFO_SYNDR_KNOWN_EXOGE_CAUSES_NOT_ELSEW_CLASSIFIED – Congenital malformation syndromes due to known exogenous causes, not elsewhere classified

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

Congenital malformation syndromes due to known exogenous causes, not elsewhere classified

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 (R11)

LabWAS

Mortality – FinRegistry

Association

Females

Males

Mortality risk

Relationships between endpoints