rs2409784

Positions:

• chr8-11539347-A-C
• chr8-11539347-A-G
• chr8-11539347-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001715.3(BLK):​c.-1-3877A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,972 control chromosomes in the GnomAD database, including 21,505 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 0.52 (21505 hom., cov: 32)
• Consequence: BLK NM_001715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

Genes affected

BLK (HGNC:1057): (BLK proto-oncogene, Src family tyrosine kinase) This gene encodes a nonreceptor tyrosine-kinase of the src family of proto-oncogenes that are typically involved in cell proliferation and differentiation. The protein has a role in B-cell receptor signaling and B-cell development. The protein also stimulates insulin synthesis and secretion in response to glucose and enhances the expression of several pancreatic beta-cell transcription factors. [provided by RefSeq, Aug 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLK	NM_001715.3	c.-1-3877A>C		intron_variant		ENST00000259089.9	NP_001706.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BLK	ENST00000259089.9	c.-1-3877A>C		intron_variant		1	NM_001715.3	ENSP00000259089	P1
BLK	ENST00000645242.1	n.275-6705A>C		intron_variant, non_coding_transcript_variant
BLK	ENST00000696154.2	n.275-6705A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78368 AN: 151856 Hom.: 21475 Cov.: 32

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.516 AC: 78431 AN: 151972 Hom.: 21505 Cov.: 32 AF XY: 0.532 AC XY: 39561 AN XY: 74298

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.537

Alfa AF: 0.480 Hom.: 11509

Bravo AF: 0.519

Asia WGS AF: 0.806 AC: 2799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.20
DANN	Benign	0.50

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

Other links and lift over

dbSNP: rs2409784; hg19: chr8-11396856;