dbSNP rs2955162: HSD17B2:c.803-2903C>T (chr16-82095172-C-T) – 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.803-2903C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,024 control chromosomes in the GnomAD database, including 4,833 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 0.25 ( 4828 hom., cov: 32)

Exomes 𝑓: 0.31 ( 5 hom. )

Consequence

HSD17B2
NM_002153.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.35

Publications

13 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=-0.95).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSD17B2	NM_002153.3 link	c.803-2903C>T		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.803-2903C>T	intron_variant	Intron 4 of 4	1	NM_002153.3	ENSP00000199936.4	P37059
HSD17B2	ENST00000566838.2 link	c.*3996C>T	3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000456471.1	H3BRZ6
HSD17B2	ENST00000568090.5 link	c.395-2903C>T	intron_variant	Intron 4 of 4	3		ENSP00000456529.1	H3BS44
HSD17B2-AS1	ENST00000567021.2 link	n.44-23983G>A	intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.248

AC:

37606

AN:

151844

Hom.:

4818

Cov.:

show subpopulations

Gnomad AFR

AF:

0.238

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.193

Gnomad ASJ

AF:

0.245

Gnomad EAS

AF:

0.107

Gnomad SAS

AF:

0.353

Gnomad FIN

AF:

0.268

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.265

Gnomad OTH

AF:

0.243

GnomAD4 exome

AF:

0.306

AC:

AN:

Hom.:

Cov.:

AF XY:

0.321

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.367

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.233

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.569

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.248

AC:

37642

AN:

151962

Hom.:

4828

Cov.:

AF XY:

0.247

AC XY:

18350

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.238

AC:

9865

AN:

41440

American (AMR)

AF:

0.193

AC:

2939

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.245

AC:

849

AN:

3464

East Asian (EAS)

AF:

0.106

AC:

548

AN:

5178

South Asian (SAS)

AF:

0.352

AC:

1688

AN:

4800

European-Finnish (FIN)

AF:

0.268

AC:

2821

AN:

10542

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.265

AC:

18036

AN:

67958

Other (OTH)

AF:

0.246

AC:

520

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1414

2829

4243

5658

7072

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

396

792

1188

1584

1980

<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:

0.260

Hom.:

9557

Bravo

AF:

0.240

Asia WGS

AF:

0.275

AC:

956

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.030

(source)

DANN

Benign

0.61

PhyloP100

-3.4

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over