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GeneBe

rs13277113

Variant summary

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

The ENST00000645242.1(BLK):n.274+4510G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 151,694 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: 33)

Consequence

BLK
ENST00000645242.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0750
Variant links:
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]

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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=-0.78).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BLKENST00000645242.1 linkuse as main transcriptn.274+4510G>A intron_variant, non_coding_transcript_variant
BLKENST00000696154.2 linkuse as main transcriptn.274+4510G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.258
AC:
39115
AN:
151576
Hom.:
6363
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.140
Gnomad AMI
AF:
0.193
Gnomad AMR
AF:
0.444
Gnomad ASJ
AF:
0.147
Gnomad EAS
AF:
0.703
Gnomad SAS
AF:
0.341
Gnomad FIN
AF:
0.272
Gnomad MID
AF:
0.184
Gnomad NFE
AF:
0.253
Gnomad OTH
AF:
0.255
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.258
AC:
39153
AN:
151694
Hom.:
6383
Cov.:
33
AF XY:
0.266
AC XY:
19705
AN XY:
74162
show subpopulations
Gnomad4 AFR
AF:
0.139
Gnomad4 AMR
AF:
0.445
Gnomad4 ASJ
AF:
0.147
Gnomad4 EAS
AF:
0.704
Gnomad4 SAS
AF:
0.341
Gnomad4 FIN
AF:
0.272
Gnomad4 NFE
AF:
0.253
Gnomad4 OTH
AF:
0.265
Alfa
AF:
0.262
Hom.:
13702
Bravo
AF:
0.272
Asia WGS
AF:
0.523
AC:
1816
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
Cadd
Benign
1.1
Dann
Benign
0.79

Splicing

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.

Other links and lift over

dbSNP: rs13277113; hg19: chr8-11349186; COSMIC: COSV52052926; COSMIC: COSV52052926; API