rs1382568

Variant names:

• chr8-11493711-A-C
• rs1382568
• ENST00000645242.1:n.274+6544A>C

Your query was ambiguous. Multiple possible variants found:

• chr8-11493711-A-C
• chr8-11493711-A-G
• chr8-11493711-A-T

Variant summary

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

The ENST00000645242.1(BLK):​n.274+6544A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,852 control chromosomes in the GnomAD database, including 7,043 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 0.28 (7043 hom., cov: 31)
• Consequence: BLK ENST00000645242.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 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+6544A>C		intron_variant	Intron 1 of 11
BLK	ENST00000696154.2	n.274+6544A>C		intron_variant	Intron 1 of 11

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42014 AN: 151734 Hom.: 7018 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.277 AC: 42079 AN: 151852 Hom.: 7043 Cov.: 31 AF XY: 0.285 AC XY: 21136 AN XY: 74212

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.290

Alfa AF: 0.707 Hom.: 10972

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.32
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1382568; hg19: chr8-11351220;