Variant chr19-577782-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The ENST00000333511.9(BSG):c.76G>T(p.Val26Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00761 in 1,417,762 control chromosomes in the GnomAD database, including 59 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0064 ( 7 hom., cov: 33)

Exomes 𝑓: 0.0078 ( 52 hom. )

Consequence

BSG
ENST00000333511.9 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.164

Variant links:

Genes affected

BSG (HGNC:1116): (basigin (Ok blood group)) The protein encoded by this gene, basigin, is a plasma membrane protein that is important in spermatogenesis, embryo implantation, neural network formation, and tumor progression. Basigin is also a member of the immunoglobulin superfamily, ubiquitously expressed in various tissues. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2020]

BSG links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005343199).

BP6

Variant 19-577782-G-T is Benign according to our data. Variant chr19-577782-G-T is described in ClinVar as [Benign]. Clinvar id is 3042170.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAd4 at 7 BG gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BSG	NM_001728.4 linkuse as main transcript	c.76G>T	p.Val26Phe	missense_variant	2/9	ENST00000333511.9	NP_001719.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BSG	ENST00000333511.9 linkuse as main transcript	c.76G>T	p.Val26Phe	missense_variant	2/9	1	NM_001728.4	ENSP00000333769	P1	P35613-1

Frequencies

GnomAD3 genomes

AF:

0.00637

AC:

970

AN:

152198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00159

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00935

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00630

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00985

Gnomad OTH

AF:

0.00860

GnomAD3 exomes

AF:

0.00548

AC:

338

AN:

61678

Hom.:

AF XY:

0.00540

AC XY:

169

AN XY:

31288

show subpopulations

Gnomad AFR exome

AF:

0.000384

Gnomad AMR exome

AF:

0.00659

Gnomad ASJ exome

AF:

0.00166

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000340

Gnomad FIN exome

AF:

0.00563

Gnomad NFE exome

AF:

0.00915

Gnomad OTH exome

AF:

0.00476

GnomAD4 exome

AF:

0.00776

AC:

9816

AN:

1265446

Hom.:

Cov.:

AF XY:

0.00763

AC XY:

4662

AN XY:

610796

show subpopulations

Gnomad4 AFR exome

AF:

0.00116

Gnomad4 AMR exome

AF:

0.00620

Gnomad4 ASJ exome

AF:

0.00112

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000227

Gnomad4 FIN exome

AF:

0.00587

Gnomad4 NFE exome

AF:

0.00895

Gnomad4 OTH exome

AF:

0.00622

GnomAD4 genome

AF:

0.00637

AC:

970

AN:

152316

Hom.:

Cov.:

AF XY:

0.00635

AC XY:

473

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.00159

Gnomad4 AMR

AF:

0.00934

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00630

Gnomad4 NFE

AF:

0.00985

Gnomad4 OTH

AF:

0.00851

Alfa

AF:

0.00520

Hom.:

Bravo

AF:

0.00571

TwinsUK

AF:

0.00431

AC:

ALSPAC

AF:

0.00856

AC:

ESP6500AA

AF:

0.00216

AC:

ESP6500EA

AF:

0.00654

AC:

ExAC

AF:

0.00198

AC:

195

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

BSG-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 02, 2024

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.54

Eigen

Benign

-0.60

Eigen_PC

Benign

-0.96

FATHMM_MKL

Benign

0.013

LIST_S2

Benign

0.75

MetaRNN

Benign

0.0053

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.4

MutationTaster

Benign

1.0

N;N;N;N

PrimateAI

Uncertain

0.63

PROVEAN

Benign

-2.4

REVEL

Benign

0.13

Sift

Uncertain

0.0030

Sift4G

Uncertain

0.011

Polyphen

0.95

Vest4

0.22

MVP

0.12

MPC

0.57

ClinPred

0.075

GERP RS

-6.3

Varity_R

0.29

gMVP

0.32

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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