Variant rs2066486 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000197.2(HSD17B3):c.672+33A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 1,608,480 control chromosomes in the GnomAD database, including 56,594 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5529 hom., cov: 32)

Exomes 𝑓: 0.26 ( 51065 hom. )

Consequence

HSD17B3
NM_000197.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.308

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 9-96244296-T-C is Benign according to our data. Variant chr9-96244296-T-C is described in ClinVar as [Benign]. Clinvar id is 255510.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HSD17B3	NM_000197.2 linkuse as main transcript	c.672+33A>G		intron_variant		ENST00000375263.8	NP_000188.1
SLC35D2-HSD17B3	NR_182427.1 linkuse as main transcript	n.3439+33A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HSD17B3	ENST00000375263.8 linkuse as main transcript	c.672+33A>G		intron_variant		1	NM_000197.2	ENSP00000364412	P1	P37058-1

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39993

AN:

151978

Hom.:

5524

Cov.:

show subpopulations

Gnomad AFR

AF:

0.302

Gnomad AMI

AF:

0.307

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.278

Gnomad EAS

AF:

0.0284

Gnomad SAS

AF:

0.131

Gnomad FIN

AF:

0.287

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.275

Gnomad OTH

AF:

0.256

GnomAD3 exomes

AF:

0.223

AC:

56111

AN:

251464

Hom.:

7292

AF XY:

0.223

AC XY:

30361

AN XY:

135910

show subpopulations

Gnomad AFR exome

AF:

0.309

Gnomad AMR exome

AF:

0.127

Gnomad ASJ exome

AF:

0.289

Gnomad EAS exome

AF:

0.0278

Gnomad SAS exome

AF:

0.140

Gnomad FIN exome

AF:

0.282

Gnomad NFE exome

AF:

0.276

Gnomad OTH exome

AF:

0.253

GnomAD4 exome

AF:

0.256

AC:

373402

AN:

1456384

Hom.:

51065

Cov.:

AF XY:

0.253

AC XY:

183418

AN XY:

724952

show subpopulations

Gnomad4 AFR exome

AF:

0.311

Gnomad4 AMR exome

AF:

0.136

Gnomad4 ASJ exome

AF:

0.285

Gnomad4 EAS exome

AF:

0.0220

Gnomad4 SAS exome

AF:

0.141

Gnomad4 FIN exome

AF:

0.282

Gnomad4 NFE exome

AF:

0.275

Gnomad4 OTH exome

AF:

0.249

GnomAD4 genome

AF:

0.263

AC:

40032

AN:

152096

Hom.:

5529

Cov.:

AF XY:

0.257

AC XY:

19120

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.302

Gnomad4 AMR

AF:

0.205

Gnomad4 ASJ

AF:

0.278

Gnomad4 EAS

AF:

0.0284

Gnomad4 SAS

AF:

0.131

Gnomad4 FIN

AF:

0.287

Gnomad4 NFE

AF:

0.275

Gnomad4 OTH

AF:

0.256

Alfa

AF:

0.267

Hom.:

1857

Bravo

AF:

0.259

Asia WGS

AF:

0.106

AC:

370

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 08, 2018	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.2

DANN

Benign

0.66

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over