rs2255227

Variant summary

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

The NM_001715.3(BLK):​c.473-1714C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.949 in 162,476 control chromosomes in the GnomAD database, including 73,446 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 0.95 ( 68529 hom., cov: 37)
Exomes 𝑓: 0.98 ( 4917 hom. )

Consequence

BLK
NM_001715.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.15
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=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BLKNM_001715.3 linkuse as main transcriptc.473-1714C>T intron_variant ENST00000259089.9
LOC105379241XR_948956.3 linkuse as main transcriptn.1729G>A non_coding_transcript_exon_variant 5/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BLKENST00000259089.9 linkuse as main transcriptc.473-1714C>T intron_variant 1 NM_001715.3 P1
ENST00000602626.2 linkuse as main transcriptn.1248G>A non_coding_transcript_exon_variant 9/9

Frequencies

GnomAD3 genomes
AF:
0.946
AC:
144037
AN:
152204
Hom.:
68486
Cov.:
37
show subpopulations
Gnomad AFR
AF:
0.846
Gnomad AMI
AF:
0.998
Gnomad AMR
AF:
0.965
Gnomad ASJ
AF:
0.947
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.994
Gnomad FIN
AF:
0.998
Gnomad MID
AF:
0.927
Gnomad NFE
AF:
0.987
Gnomad OTH
AF:
0.944
GnomAD4 exome
AF:
0.984
AC:
9991
AN:
10154
Hom.:
4917
Cov.:
0
AF XY:
0.985
AC XY:
5190
AN XY:
5268
show subpopulations
Gnomad4 AFR exome
AF:
0.831
Gnomad4 AMR exome
AF:
0.972
Gnomad4 ASJ exome
AF:
0.951
Gnomad4 EAS exome
AF:
1.00
Gnomad4 SAS exome
AF:
0.998
Gnomad4 FIN exome
AF:
1.00
Gnomad4 NFE exome
AF:
0.991
Gnomad4 OTH exome
AF:
0.973
GnomAD4 genome
AF:
0.946
AC:
144138
AN:
152322
Hom.:
68529
Cov.:
37
AF XY:
0.948
AC XY:
70596
AN XY:
74488
show subpopulations
Gnomad4 AFR
AF:
0.846
Gnomad4 AMR
AF:
0.965
Gnomad4 ASJ
AF:
0.947
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.995
Gnomad4 FIN
AF:
0.998
Gnomad4 NFE
AF:
0.987
Gnomad4 OTH
AF:
0.945
Alfa
AF:
0.966
Hom.:
8843
Bravo
AF:
0.941
Asia WGS
AF:
0.984
AC:
3421
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.71
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2255227; hg19: chr8-11410538; API