Variant rs8190540 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000197.2(HSD17B3):c.386-627_386-626insAGTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 151,984 control chromosomes in the GnomAD database, including 5,301 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.26 ( 5301 hom., cov: 21)

Consequence

HSD17B3
NM_000197.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.639

Variant links:

Genes affected

HSD17B3 (HGNC:5212): (hydroxysteroid 17-beta dehydrogenase 3) This isoform of 17 beta-hydroxysteroid dehydrogenase is expressed predominantly in the testis and catalyzes the conversion of androstenedione to testosterone. It preferentially uses NADP as cofactor. Deficiency can result in male pseudohermaphroditism with gynecomastia. [provided by RefSeq, Jul 2008]

HSD17B3 links:

SLC35D2-HSD17B3 (HGNC:):

SLC35D2-HSD17B3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSD17B3	NM_000197.2 linkuse as main transcript	c.386-627_386-626insAGTT		intron_variant		ENST00000375263.8
SLC35D2-HSD17B3	NR_182427.1 linkuse as main transcript	n.3153-627_3153-626insAGTT		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD17B3	ENST00000375263.8 linkuse as main transcript	c.386-627_386-626insAGTT		intron_variant		1	NM_000197.2	P1	P37058-1

Frequencies

GnomAD3 genomes

AF:

0.258

AC:

39236

AN:

151866

Hom.:

5294

Cov.:

show subpopulations

Gnomad AFR

AF:

0.305

Gnomad AMI

AF:

0.307

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.271

Gnomad EAS

AF:

0.0281

Gnomad SAS

AF:

0.134

Gnomad FIN

AF:

0.270

Gnomad MID

AF:

0.293

Gnomad NFE

AF:

0.267

Gnomad OTH

AF:

0.245

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.258

AC:

39277

AN:

151984

Hom.:

5301

Cov.:

AF XY:

0.252

AC XY:

18722

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.305

Gnomad4 AMR

AF:

0.197

Gnomad4 ASJ

AF:

0.271

Gnomad4 EAS

AF:

0.0281

Gnomad4 SAS

AF:

0.135

Gnomad4 FIN

AF:

0.270

Gnomad4 NFE

AF:

0.267

Gnomad4 OTH

AF:

0.246

Alfa

AF:

0.259

Hom.:

644

Asia WGS

AF:

0.107

AC:

371

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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