Variant 2-20619056-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000304031.8(HS1BP3):c.1110C>T(p.Asp370=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 1,614,154 control chromosomes in the GnomAD database, including 120 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0074 ( 8 hom., cov: 33)

Exomes 𝑓: 0.010 ( 112 hom. )

Consequence

HS1BP3
ENST00000304031.8 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.286

Variant links:

Genes affected

HS1BP3 (HGNC:24979): (HCLS1 binding protein 3) The protein encoded by this gene shares similarity with mouse Hs1bp3, an Hcls1/Hs1-interacting protein that may be involved in lymphocyte activation. [provided by RefSeq, Jul 2008]

HS1BP3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 2-20619056-G-A is Benign according to our data. Variant chr2-20619056-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2650702.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.286 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
HS1BP3	NM_022460.4 linkuse as main transcript	c.1110C>T	p.Asp370=	synonymous_variant	7/7	ENST00000304031.8	NP_071905.3
HS1BP3	XM_017004696.3 linkuse as main transcript	c.920+4840C>T		intron_variant			XP_016860185.1
HS1BP3	XM_017004697.3 linkuse as main transcript	c.920+4840C>T		intron_variant			XP_016860186.1
HS1BP3	XM_017004698.2 linkuse as main transcript	c.920+4840C>T		intron_variant			XP_016860187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
HS1BP3	ENST00000304031.8 linkuse as main transcript	c.1110C>T	p.Asp370=	synonymous_variant	7/7	1	NM_022460.4	ENSP00000305193	P1
HS1BP3	ENST00000415264.5 linkuse as main transcript	c.178+4840C>T		intron_variant		3		ENSP00000387364
HS1BP3	ENST00000446825.1 linkuse as main transcript	c.302+4840C>T		intron_variant		3		ENSP00000389960
HS1BP3	ENST00000651498.1 linkuse as main transcript	c.*551C>T		3_prime_UTR_variant, NMD_transcript_variant	6/6			ENSP00000498575

Frequencies

GnomAD3 genomes

AF:

0.00743

AC:

1130

AN:

152164

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00195

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.00694

Gnomad ASJ

AF:

0.0482

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00621

Gnomad FIN

AF:

0.000848

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0103

Gnomad OTH

AF:

0.00621

GnomAD3 exomes

AF:

0.00823

AC:

2057

AN:

250028

Hom.:

AF XY:

0.00838

AC XY:

1133

AN XY:

135230

show subpopulations

Gnomad AFR exome

AF:

0.00135

Gnomad AMR exome

AF:

0.00443

Gnomad ASJ exome

AF:

0.0531

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00689

Gnomad FIN exome

AF:

0.00116

Gnomad NFE exome

AF:

0.00937

Gnomad OTH exome

AF:

0.00946

GnomAD4 exome

AF:

0.0105

AC:

15345

AN:

1461872

Hom.:

112

Cov.:

AF XY:

0.0106

AC XY:

7739

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.00111

Gnomad4 AMR exome

AF:

0.00411

Gnomad4 ASJ exome

AF:

0.0541

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00756

Gnomad4 FIN exome

AF:

0.00139

Gnomad4 NFE exome

AF:

0.0110

Gnomad4 OTH exome

AF:

0.0109

GnomAD4 genome

AF:

0.00741

AC:

1128

AN:

152282

Hom.:

Cov.:

AF XY:

0.00686

AC XY:

511

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.00195

Gnomad4 AMR

AF:

0.00693

Gnomad4 ASJ

AF:

0.0482

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00643

Gnomad4 FIN

AF:

0.000848

Gnomad4 NFE

AF:

0.0103

Gnomad4 OTH

AF:

0.00615

Alfa

AF:

0.0115

Hom.:

Bravo

AF:

0.00777

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.0135

EpiControl

AF:

0.00972

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2023

HS1BP3: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

6.9

DANN

Benign

0.89

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over