rs9693589

Variant names:

• chr8-11491452-G-A
• rs9693589
• ENST00000645242.1:n.274+4285G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-11491452-G-A
• chr8-11491452-G-C
• chr8-11491452-G-T

Variant summary

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

The ENST00000645242.1(BLK):​n.274+4285G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 151,924 control chromosomes in the GnomAD database, including 6,383 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 0.26 (6383 hom., cov: 31)
• Consequence: BLK ENST00000645242.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLK	ENST00000645242.1	n.274+4285G>A		intron_variant	Intron 1 of 11
BLK	ENST00000696154.2	n.274+4285G>A		intron_variant	Intron 1 of 11

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39093 AN: 151806 Hom.: 6363 Cov.: 31

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.258 AC: 39129 AN: 151924 Hom.: 6383 Cov.: 31 AF XY: 0.265 AC XY: 19713 AN XY: 74260

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.703

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.266

Alfa AF: 0.230 Hom.: 558

Bravo AF: 0.272

Asia WGS AF: 0.526 AC: 1828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9693589; hg19: chr8-11348961;