Variant rs7190458 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000162330.10(BCAR1):c.2361C>T(p.Leu787=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0517 in 1,613,400 control chromosomes in the GnomAD database, including 4,010 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 0.10 ( 1482 hom., cov: 33)

Exomes 𝑓: 0.046 ( 2528 hom. )

Consequence

BCAR1
ENST00000162330.10 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.883

Variant links:

Genes affected

BCAR1 (HGNC:971): (BCAR1 scaffold protein, Cas family member) The protein encoded by this gene is a member of the Crk-associated substrate (CAS) family of scaffold proteins, characterized by the presence of multiple protein-protein interaction domains and many serine and tyrosine phosphorylation sites. The encoded protein contains a Src-homology 3 (SH3) domain, a proline-rich domain, a substrate domain which contains 15 repeat of the YxxP consensus phosphorylation motif for Src family kinases, a serine-rich domain, and a bipartite Src-binding domain, which can bind both SH2 and SH3 domains. This adaptor protein functions in multiple cellular pathways, including in cell motility, apoptosis and cell cycle control. Dysregulation of this gene can have a wide range of effects, affecting different pathways, including cardiac development, vascular smooth muscle cells, liver and kidney function, endothelial migration, and cancer. [provided by RefSeq, Sep 2017]

BCAR1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP7

Synonymous conserved (PhyloP=0.883 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCAR1	NM_014567.5 linkuse as main transcript	c.2361C>T	p.Leu787=	synonymous_variant	7/7	ENST00000162330.10	NP_055382.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCAR1	ENST00000162330.10 linkuse as main transcript	c.2361C>T	p.Leu787=	synonymous_variant	7/7	1	NM_014567.5	ENSP00000162330	P4	P56945-1

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15579

AN:

152180

Hom.:

1474

Cov.:

show subpopulations

Gnomad AFR

AF:

0.248

Gnomad AMI

AF:

0.0943

Gnomad AMR

AF:

0.0798

Gnomad ASJ

AF:

0.0363

Gnomad EAS

AF:

0.0298

Gnomad SAS

AF:

0.00930

Gnomad FIN

AF:

0.0449

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0438

Gnomad OTH

AF:

0.0923

GnomAD3 exomes

AF:

0.0514

AC:

12892

AN:

250902

Hom.:

743

AF XY:

0.0455

AC XY:

6175

AN XY:

135844

show subpopulations

Gnomad AFR exome

AF:

0.261

Gnomad AMR exome

AF:

0.0435

Gnomad ASJ exome

AF:

0.0392

Gnomad EAS exome

AF:

0.0244

Gnomad SAS exome

AF:

0.00699

Gnomad FIN exome

AF:

0.0422

Gnomad NFE exome

AF:

0.0432

Gnomad OTH exome

AF:

0.0474

GnomAD4 exome

AF:

0.0464

AC:

67833

AN:

1461102

Hom.:

2528

Cov.:

AF XY:

0.0443

AC XY:

32177

AN XY:

726886

show subpopulations

Gnomad4 AFR exome

AF:

0.264

Gnomad4 AMR exome

AF:

0.0500

Gnomad4 ASJ exome

AF:

0.0388

Gnomad4 EAS exome

AF:

0.0225

Gnomad4 SAS exome

AF:

0.00667

Gnomad4 FIN exome

AF:

0.0385

Gnomad4 NFE exome

AF:

0.0439

Gnomad4 OTH exome

AF:

0.0540

GnomAD4 genome

AF:

0.102

AC:

15606

AN:

152298

Hom.:

1482

Cov.:

AF XY:

0.100

AC XY:

7446

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.248

Gnomad4 AMR

AF:

0.0800

Gnomad4 ASJ

AF:

0.0363

Gnomad4 EAS

AF:

0.0299

Gnomad4 SAS

AF:

0.00931

Gnomad4 FIN

AF:

0.0449

Gnomad4 NFE

AF:

0.0438

Gnomad4 OTH

AF:

0.0922

Alfa

AF:

0.0577

Hom.:

698

Bravo

AF:

0.113

Asia WGS

AF:

0.0450

AC:

159

AN:

3478

EpiCase

AF:

0.0384

EpiControl

AF:

0.0407

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

5.3

DANN

Benign

0.91

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