Variant rs383711 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014234.5(HSD17B8):c.694+45G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0866 in 1,601,390 control chromosomes in the GnomAD database, including 10,770 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 0.093 ( 1211 hom., cov: 31)

Exomes 𝑓: 0.086 ( 9559 hom. )

Consequence

HSD17B8
NM_014234.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.384

Variant links:

Genes affected

HSD17B8 (HGNC:3554): (hydroxysteroid 17-beta dehydrogenase 8) In mice, the Ke6 protein is a 17-beta-hydroxysteroid dehydrogenase that can regulate the concentration of biologically active estrogens and androgens. It is preferentially an oxidative enzyme and inactivates estradiol, testosterone, and dihydrotestosterone. However, the enzyme has some reductive activity and can synthesize estradiol from estrone. The protein encoded by this gene is similar to Ke6 and is a member of the short-chain dehydrogenase superfamily. An alternatively spliced transcript of this gene has been detected, but the full-length nature of this variant has not been determined. [provided by RefSeq, Jul 2008]

HSD17B8 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HSD17B8	NM_014234.5 linkuse as main transcript	c.694+45G>A		intron_variant		ENST00000374662.4	NP_055049.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HSD17B8	ENST00000374662.4 linkuse as main transcript	c.694+45G>A		intron_variant		1	NM_014234.5	ENSP00000363794	P1
HSD17B8	ENST00000469186.1 linkuse as main transcript	n.858+45G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0934

AC:

14202

AN:

152104

Hom.:

1200

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0905

Gnomad AMI

AF:

0.0526

Gnomad AMR

AF:

0.0832

Gnomad ASJ

AF:

0.0436

Gnomad EAS

AF:

0.515

Gnomad SAS

AF:

0.0889

Gnomad FIN

AF:

0.0852

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0693

Gnomad OTH

AF:

0.111

GnomAD3 exomes

AF:

0.106

AC:

25809

AN:

242872

Hom.:

3137

AF XY:

0.103

AC XY:

13718

AN XY:

133188

show subpopulations

Gnomad AFR exome

AF:

0.0883

Gnomad AMR exome

AF:

0.0751

Gnomad ASJ exome

AF:

0.0449

Gnomad EAS exome

AF:

0.526

Gnomad SAS exome

AF:

0.0781

Gnomad FIN exome

AF:

0.0790

Gnomad NFE exome

AF:

0.0684

Gnomad OTH exome

AF:

0.0866

GnomAD4 exome

AF:

0.0859

AC:

124490

AN:

1449168

Hom.:

9559

Cov.:

AF XY:

0.0850

AC XY:

61322

AN XY:

721334

show subpopulations

Gnomad4 AFR exome

AF:

0.0880

Gnomad4 AMR exome

AF:

0.0772

Gnomad4 ASJ exome

AF:

0.0468

Gnomad4 EAS exome

AF:

0.525

Gnomad4 SAS exome

AF:

0.0808

Gnomad4 FIN exome

AF:

0.0771

Gnomad4 NFE exome

AF:

0.0719

Gnomad4 OTH exome

AF:

0.0922

GnomAD4 genome

AF:

0.0934

AC:

14221

AN:

152222

Hom.:

1211

Cov.:

AF XY:

0.0952

AC XY:

7085

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0904

Gnomad4 AMR

AF:

0.0832

Gnomad4 ASJ

AF:

0.0436

Gnomad4 EAS

AF:

0.516

Gnomad4 SAS

AF:

0.0890

Gnomad4 FIN

AF:

0.0852

Gnomad4 NFE

AF:

0.0693

Gnomad4 OTH

AF:

0.120

Alfa

AF:

0.0706

Hom.:

362

Bravo

AF:

0.0974

Asia WGS

AF:

0.241

AC:

835

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

DANN

Benign

0.71

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over