dbSNP rs4445895: HSD17B2:c.-133T>A (chr16-82035292-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_002153.3(HSD17B2):c.-133T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

HSD17B2
NM_002153.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0890

Publications

15 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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSD17B2	NM_002153.3 link	c.-133T>A		5_prime_UTR_variant	Exon 1 of 5	ENST00000199936.9	NP_002144.1	P37059
HSD17B2	XM_047434049.1 link	c.-133T>A		5_prime_UTR_variant	Exon 1 of 4		XP_047290005.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
HSD17B2	ENST00000199936.9 link	c.-133T>A	5_prime_UTR_variant	Exon 1 of 5	1	NM_002153.3	ENSP00000199936.4	P37059
HSD17B2	ENST00000566213.1 link	c.-133T>A	5_prime_UTR_variant	Exon 1 of 2	3		ENSP00000457943.1	H3BV42
HSD17B2	ENST00000563491.5 link	c.-144+144T>A	intron_variant	Intron 1 of 2	3		ENSP00000455992.1	H3BQY3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

582524

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

302342

African (AFR)

AF:

0.00

AC:

AN:

15432

American (AMR)

AF:

0.00

AC:

AN:

21244

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14700

East Asian (EAS)

AF:

0.00

AC:

AN:

33348

South Asian (SAS)

AF:

0.00

AC:

AN:

50078

European-Finnish (FIN)

AF:

0.00

AC:

AN:

33508

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2216

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

381416

Other (OTH)

AF:

0.00

AC:

AN:

30582

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

5.7

(source)

DANN

Benign

0.65

PhyloP100

-0.089

PromoterAI

-0.0040

Neutral

(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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over