Variant 1-119514535-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000369413.8(HSD3B1):c.1012C>T(p.Leu338=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 1,613,554 control chromosomes in the GnomAD database, including 159,076 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 0.36 ( 12170 hom., cov: 30)

Exomes 𝑓: 0.44 ( 146906 hom. )

Consequence

HSD3B1
ENST00000369413.8 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.25

Variant links:

Genes affected

HSD3B1 (HGNC:5217): (hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1) The protein encoded by this gene is an enzyme that catalyzes the oxidative conversion of delta-5-3-beta-hydroxysteroid precursors into delta-4-ketosteroids, which leads to the production of all classes of steroid hormones. The encoded protein also catalyzes the interconversion of 3-beta-hydroxy- and 3-keto-5-alpha-androstane steroids. [provided by RefSeq, Jun 2016]

HSD3B1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP7

Synonymous conserved (PhyloP=1.25 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HSD3B1	NM_000862.3 linkuse as main transcript	c.1012C>T	p.Leu338=	synonymous_variant	4/4	ENST00000369413.8	NP_000853.1
HSD3B1	NM_001328615.1 linkuse as main transcript	c.1012C>T	p.Leu338=	synonymous_variant	4/4		NP_001315544.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HSD3B1	ENST00000369413.8 linkuse as main transcript	c.1012C>T	p.Leu338=	synonymous_variant	4/4	1	NM_000862.3	ENSP00000358421	P1
HSD3B1	ENST00000528909.1 linkuse as main transcript	c.1012C>T	p.Leu338=	synonymous_variant	3/3	1		ENSP00000432268	P1

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54643

AN:

151654

Hom.:

12174

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0946

Gnomad AMI

AF:

0.656

Gnomad AMR

AF:

0.475

Gnomad ASJ

AF:

0.345

Gnomad EAS

AF:

0.657

Gnomad SAS

AF:

0.414

Gnomad FIN

AF:

0.556

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.437

Gnomad OTH

AF:

0.365

GnomAD3 exomes

AF:

0.451

AC:

113324

AN:

251016

Hom.:

27745

AF XY:

0.451

AC XY:

61213

AN XY:

135634

show subpopulations

Gnomad AFR exome

AF:

0.0811

Gnomad AMR exome

AF:

0.569

Gnomad ASJ exome

AF:

0.356

Gnomad EAS exome

AF:

0.672

Gnomad SAS exome

AF:

0.410

Gnomad FIN exome

AF:

0.539

Gnomad NFE exome

AF:

0.436

Gnomad OTH exome

AF:

0.447

GnomAD4 exome

AF:

0.441

AC:

644912

AN:

1461782

Hom.:

146906

Cov.:

AF XY:

0.440

AC XY:

320134

AN XY:

727200

show subpopulations

Gnomad4 AFR exome

AF:

0.0739

Gnomad4 AMR exome

AF:

0.555

Gnomad4 ASJ exome

AF:

0.359

Gnomad4 EAS exome

AF:

0.663

Gnomad4 SAS exome

AF:

0.410

Gnomad4 FIN exome

AF:

0.537

Gnomad4 NFE exome

AF:

0.441

Gnomad4 OTH exome

AF:

0.432

GnomAD4 genome

AF:

0.360

AC:

54644

AN:

151772

Hom.:

12170

Cov.:

AF XY:

0.372

AC XY:

27559

AN XY:

74148

show subpopulations

Gnomad4 AFR

AF:

0.0943

Gnomad4 AMR

AF:

0.475

Gnomad4 ASJ

AF:

0.345

Gnomad4 EAS

AF:

0.656

Gnomad4 SAS

AF:

0.415

Gnomad4 FIN

AF:

0.556

Gnomad4 NFE

AF:

0.437

Gnomad4 OTH

AF:

0.366

Alfa

AF:

0.406

Hom.:

4269

Bravo

AF:

0.346

Asia WGS

AF:

0.473

AC:

1646

AN:

3478

EpiCase

AF:

0.423

EpiControl

AF:

0.423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

6.2

DANN

Benign

0.60

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