Variant rs1862737 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001170719.3(BCAR1):c.-7T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 1,563,056 control chromosomes in the GnomAD database, including 226,531 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 0.49 ( 19303 hom., cov: 32)

Exomes 𝑓: 0.54 ( 207228 hom. )

Consequence

BCAR1
NM_001170719.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.454

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:

ENSG00000280152 (HGNC:):

ENSG00000280152 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.622 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.12+3405T>G		intron_variant		ENST00000162330.10	NP_055382.2	P56945-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCAR1	ENST00000162330.10 linkuse as main transcript	c.12+3405T>G		intron_variant		1	NM_014567.5	ENSP00000162330.5		P56945-1

Frequencies

GnomAD3 genomes

AF:

0.494

AC:

74944

AN:

151836

Hom.:

19292

Cov.:

show subpopulations

Gnomad AFR

AF:

0.344

Gnomad AMI

AF:

0.377

Gnomad AMR

AF:

0.632

Gnomad ASJ

AF:

0.482

Gnomad EAS

AF:

0.588

Gnomad SAS

AF:

0.534

Gnomad FIN

AF:

0.593

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.529

Gnomad OTH

AF:

0.529

GnomAD3 exomes

AF:

0.560

AC:

130694

AN:

233566

Hom.:

37959

AF XY:

0.554

AC XY:

70970

AN XY:

128006

show subpopulations

Gnomad AFR exome

AF:

0.340

Gnomad AMR exome

AF:

0.755

Gnomad ASJ exome

AF:

0.478

Gnomad EAS exome

AF:

0.583

Gnomad SAS exome

AF:

0.540

Gnomad FIN exome

AF:

0.585

Gnomad NFE exome

AF:

0.535

Gnomad OTH exome

AF:

0.554

GnomAD4 exome

AF:

0.539

AC:

760115

AN:

1411102

Hom.:

207228

Cov.:

AF XY:

0.538

AC XY:

378961

AN XY:

704638

show subpopulations

Gnomad4 AFR exome

AF:

0.344

Gnomad4 AMR exome

AF:

0.737

Gnomad4 ASJ exome

AF:

0.482

Gnomad4 EAS exome

AF:

0.590

Gnomad4 SAS exome

AF:

0.541

Gnomad4 FIN exome

AF:

0.586

Gnomad4 NFE exome

AF:

0.535

Gnomad4 OTH exome

AF:

0.527

GnomAD4 genome

AF:

0.494

AC:

74995

AN:

151954

Hom.:

19303

Cov.:

AF XY:

0.500

AC XY:

37106

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.344

Gnomad4 AMR

AF:

0.632

Gnomad4 ASJ

AF:

0.482

Gnomad4 EAS

AF:

0.588

Gnomad4 SAS

AF:

0.535

Gnomad4 FIN

AF:

0.593

Gnomad4 NFE

AF:

0.529

Gnomad4 OTH

AF:

0.528

Alfa

AF:

0.521

Hom.:

36418

Bravo

AF:

0.490

Asia WGS

AF:

0.585

AC:

2036

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.70

DANN

Benign

0.55

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.15

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