rs13337397

Variant names:

• chr16-75261741-C-A
• rs13337397
• NM_001170714.3:c.150+2610G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001170714.3(BCAR1):​c.150+2610G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,200 control chromosomes in the GnomAD database, including 1,794 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 0.14 (1794 hom., cov: 33)
• Consequence: BCAR1 NM_001170714.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 20 publications found

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]

LOC105371344 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCAR1	NM_001170714.3	c.150+2610G>T		intron_variant	Intron 2 of 7		NP_001164185.1
BCAR1	NM_001170715.3	c.66+6174G>T		intron_variant	Intron 1 of 6		NP_001164186.1
BCAR1	NM_001170716.3	c.66+4973G>T		intron_variant	Intron 1 of 6		NP_001164187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCAR1	ENST00000418647.7	c.150+2610G>T		intron_variant	Intron 2 of 7	2		ENSP00000391669.3
BCAR1	ENST00000393422.6	c.66+6174G>T		intron_variant	Intron 1 of 6	2		ENSP00000377074.2
BCAR1	ENST00000420641.7	c.66+4973G>T		intron_variant	Intron 1 of 6	2		ENSP00000392708.3

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21571 AN: 152080 Hom.: 1792 Cov.: 33

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0789

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.126

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.142 AC: 21583 AN: 152200 Hom.: 1794 Cov.: 33 AF XY: 0.142 AC XY: 10543 AN XY: 74412

African (AFR) AF: 0.207 AC: 8605 AN: 41508

American (AMR) AF: 0.107 AC: 1632 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0789 AC: 274 AN: 3472

East Asian (EAS) AF: 0.322 AC: 1661 AN: 5162

South Asian (SAS) AF: 0.125 AC: 603 AN: 4818

European-Finnish (FIN) AF: 0.140 AC: 1485 AN: 10618

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6926 AN: 68010

Other (OTH) AF: 0.127 AC: 269 AN: 2112

Alfa AF: 0.112 Hom.: 539

Bravo AF: 0.145

Asia WGS AF: 0.225 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.7
DANN	Benign	0.82
PhyloP100		0.062
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13337397; hg19: chr16-75295639;