Variant chr8-11561264-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001715.3(BLK):c.1030-38C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 1,599,138 control chromosomes in the GnomAD database, including 127,054 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 13181 hom., cov: 33)

Exomes 𝑓: 0.38 ( 113873 hom. )

Consequence

BLK
NM_001715.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.0220

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]

BLK links:

BLK (HGNC:):

BLK links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 8-11561264-C-T is Benign according to our data. Variant chr8-11561264-C-T is described in ClinVar as [Benign]. Clinvar id is 1192426.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLK	NM_001715.3 linkuse as main transcript	c.1030-38C>T		intron_variant		ENST00000259089.9	NP_001706.2	P51451Q05D26

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BLK	ENST00000259089.9 linkuse as main transcript	c.1030-38C>T		intron_variant		1	NM_001715.3	ENSP00000259089.4		P51451

Frequencies

GnomAD3 genomes

AF:

0.399

AC:

60638

AN:

151914

Hom.:

13161

Cov.:

show subpopulations

Gnomad AFR

AF:

0.361

Gnomad AMI

AF:

0.563

Gnomad AMR

AF:

0.502

Gnomad ASJ

AF:

0.328

Gnomad EAS

AF:

0.924

Gnomad SAS

AF:

0.469

Gnomad FIN

AF:

0.430

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.352

Gnomad OTH

AF:

0.393

GnomAD3 exomes

AF:

0.444

AC:

101057

AN:

227774

Hom.:

25324

AF XY:

0.439

AC XY:

53921

AN XY:

122940

show subpopulations

Gnomad AFR exome

AF:

0.358

Gnomad AMR exome

AF:

0.591

Gnomad ASJ exome

AF:

0.320

Gnomad EAS exome

AF:

0.923

Gnomad SAS exome

AF:

0.457

Gnomad FIN exome

AF:

0.410

Gnomad NFE exome

AF:

0.346

Gnomad OTH exome

AF:

0.409

GnomAD4 exome

AF:

0.383

AC:

554266

AN:

1447106

Hom.:

113873

Cov.:

AF XY:

0.383

AC XY:

275386

AN XY:

718498

show subpopulations

Gnomad4 AFR exome

AF:

0.356

Gnomad4 AMR exome

AF:

0.583

Gnomad4 ASJ exome

AF:

0.324

Gnomad4 EAS exome

AF:

0.919

Gnomad4 SAS exome

AF:

0.455

Gnomad4 FIN exome

AF:

0.408

Gnomad4 NFE exome

AF:

0.351

Gnomad4 OTH exome

AF:

0.400

GnomAD4 genome

AF:

0.399

AC:

60699

AN:

152032

Hom.:

13181

Cov.:

AF XY:

0.409

AC XY:

30408

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.361

Gnomad4 AMR

AF:

0.503

Gnomad4 ASJ

AF:

0.328

Gnomad4 EAS

AF:

0.924

Gnomad4 SAS

AF:

0.468

Gnomad4 FIN

AF:

0.430

Gnomad4 NFE

AF:

0.352

Gnomad4 OTH

AF:

0.401

Alfa

AF:

0.356

Hom.:

1871

Bravo

AF:

0.410

Asia WGS

AF:

0.670

AC:

2328

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 09, 2018	- -

Maturity-onset diabetes of the young type 11

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Systemic lupus erythematosus

Benign:1

Benign, criteria provided, single submitter

research

Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic

BLK gene is associated with Systemic lupus erythematosus, sjogren's syndrome and other systemic inflammatory conditions. However no sufficient evidence is found to ascertain the role of this particular variant rs4841561, yet. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.3

DANN

Uncertain

1.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over