Genetic Variant NM_002153.3:c.803-102C>G (chr16-82097973-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002153.3(HSD17B2):c.803-102C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.909 in 1,057,096 control chromosomes in the GnomAD database, including 442,650 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.84 ( 54747 hom., cov: 30)

Exomes 𝑓: 0.92 ( 387903 hom. )

Consequence

HSD17B2
NM_002153.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0390

Publications

7 publications found

Variant links:

Genes affected

HSD17B2 (HGNC:5211): (hydroxysteroid 17-beta dehydrogenase 2) Enables estradiol 17-beta-dehydrogenase activity and testosterone dehydrogenase (NAD+) activity. Involved in response to retinoic acid. Predicted to be located in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

HSD17B2 links:

HSD17B2-AS1 (HGNC:56281): (HSD17B2 antisense RNA 1)

HSD17B2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSD17B2	NM_002153.3 link	c.803-102C>G		intron_variant	Intron 4 of 4	ENST00000199936.9	NP_002144.1	P37059

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
HSD17B2	ENST00000199936.9 link	c.803-102C>G	intron_variant	Intron 4 of 4	1	NM_002153.3	ENSP00000199936.4	P37059
HSD17B2	ENST00000566838.2 link	c.*6797C>G	3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000456471.1	H3BRZ6
HSD17B2	ENST00000568090.5 link	c.395-102C>G	intron_variant	Intron 4 of 4	3		ENSP00000456529.1	H3BS44
HSD17B2-AS1	ENST00000567021.2 link	n.44-26784G>C	intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.839

AC:

127126

AN:

151582

Hom.:

54723

Cov.:

show subpopulations

Gnomad AFR

AF:

0.667

Gnomad AMI

AF:

0.971

Gnomad AMR

AF:

0.738

Gnomad ASJ

AF:

0.950

Gnomad EAS

AF:

0.668

Gnomad SAS

AF:

0.853

Gnomad FIN

AF:

0.938

Gnomad MID

AF:

0.918

Gnomad NFE

AF:

0.953

Gnomad OTH

AF:

0.867

GnomAD4 exome

AF:

0.921

AC:

834191

AN:

905396

Hom.:

387903

Cov.:

AF XY:

0.922

AC XY:

418873

AN XY:

454524

show subpopulations

African (AFR)

AF:

0.644

AC:

13183

AN:

20476

American (AMR)

AF:

0.657

AC:

13824

AN:

21048

Ashkenazi Jewish (ASJ)

AF:

0.941

AC:

15063

AN:

16014

East Asian (EAS)

AF:

0.655

AC:

21663

AN:

33050

South Asian (SAS)

AF:

0.862

AC:

38453

AN:

44630

European-Finnish (FIN)

AF:

0.931

AC:

42148

AN:

45252

Middle Eastern (MID)

AF:

0.913

AC:

2546

AN:

2790

European-Non Finnish (NFE)

AF:

0.955

AC:

651308

AN:

682240

Other (OTH)

AF:

0.902

AC:

36003

AN:

39896

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

2733

5466

8199

10932

13665

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11840

23680

35520

47360

59200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.838

AC:

127193

AN:

151700

Hom.:

54747

Cov.:

AF XY:

0.834

AC XY:

61842

AN XY:

74124

show subpopulations

African (AFR)

AF:

0.667

AC:

27530

AN:

41276

American (AMR)

AF:

0.738

AC:

11228

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.950

AC:

3295

AN:

3468

East Asian (EAS)

AF:

0.668

AC:

3441

AN:

5154

South Asian (SAS)

AF:

0.854

AC:

4108

AN:

4808

European-Finnish (FIN)

AF:

0.938

AC:

9866

AN:

10518

Middle Eastern (MID)

AF:

0.915

AC:

269

AN:

294

European-Non Finnish (NFE)

AF:

0.953

AC:

64740

AN:

67932

Other (OTH)

AF:

0.865

AC:

1830

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

884

1767

2651

3534

4418

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

874

1748

2622

3496

4370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.873

Hom.:

3044

Bravo

AF:

0.816

Asia WGS

AF:

0.760

AC:

2638

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.12

(source)

DANN

Benign

0.36

PhyloP100

-0.039

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over