Variant chr19-579627-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The ENST00000333511.9(BSG):c.543C>T(p.Asp181=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 1,611,332 control chromosomes in the GnomAD database, including 12,594 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.14 ( 1694 hom., cov: 34)

Exomes 𝑓: 0.11 ( 10900 hom. )

Consequence

BSG
ENST00000333511.9 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.244

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 19-579627-C-T is Benign according to our data. Variant chr19-579627-C-T is described in ClinVar as [Benign]. Clinvar id is 3059371.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.244 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BSG	NM_001728.4 linkuse as main transcript	c.543C>T	p.Asp181=	synonymous_variant	3/9	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.543C>T	p.Asp181=	synonymous_variant	3/9	1	NM_001728.4	ENSP00000333769	P1	P35613-1

Frequencies

GnomAD3 genomes

AF:

0.139

AC:

21110

AN:

152142

Hom.:

1692

Cov.:

show subpopulations

Gnomad AFR

AF:

0.182

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.0970

Gnomad ASJ

AF:

0.143

Gnomad EAS

AF:

0.219

Gnomad SAS

AF:

0.263

Gnomad FIN

AF:

0.182

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.0990

Gnomad OTH

AF:

0.134

GnomAD3 exomes

AF:

0.143

AC:

35090

AN:

245942

Hom.:

3128

AF XY:

0.148

AC XY:

19773

AN XY:

133792

show subpopulations

Gnomad AFR exome

AF:

0.186

Gnomad AMR exome

AF:

0.0919

Gnomad ASJ exome

AF:

0.149

Gnomad EAS exome

AF:

0.229

Gnomad SAS exome

AF:

0.270

Gnomad FIN exome

AF:

0.174

Gnomad NFE exome

AF:

0.0965

Gnomad OTH exome

AF:

0.129

GnomAD4 exome

AF:

0.110

AC:

160182

AN:

1459072

Hom.:

10900

Cov.:

AF XY:

0.115

AC XY:

83404

AN XY:

725816

show subpopulations

Gnomad4 AFR exome

AF:

0.184

Gnomad4 AMR exome

AF:

0.0917

Gnomad4 ASJ exome

AF:

0.146

Gnomad4 EAS exome

AF:

0.186

Gnomad4 SAS exome

AF:

0.267

Gnomad4 FIN exome

AF:

0.166

Gnomad4 NFE exome

AF:

0.0884

Gnomad4 OTH exome

AF:

0.128

GnomAD4 genome

AF:

0.139

AC:

21123

AN:

152260

Hom.:

1694

Cov.:

AF XY:

0.145

AC XY:

10767

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.181

Gnomad4 AMR

AF:

0.0969

Gnomad4 ASJ

AF:

0.143

Gnomad4 EAS

AF:

0.219

Gnomad4 SAS

AF:

0.263

Gnomad4 FIN

AF:

0.182

Gnomad4 NFE

AF:

0.0990

Gnomad4 OTH

AF:

0.138

Alfa

AF:

0.105

Hom.:

1387

Bravo

AF:

0.133

Asia WGS

AF:

0.242

AC:

842

AN:

3478

EpiCase

AF:

0.101

EpiControl

AF:

0.105

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

Oct 31, 2019

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

BayesDel_noAF

Benign

-0.68

CADD

Benign

7.6

DANN

Benign

0.40

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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