rs13277113

Variant summary

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

The ENST00000645242(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 151576 control chromosomes in the gnomAD Genomes database, including 6363 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 ( 6363 hom., cov: 33)

Consequence

BLK
ENST00000645242 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0750

Links

BLK (HGNC:1057):

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

GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 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
BLK	ENST00000645242.1 linkuse as main transcript	n.274+4510G>A		intron_variant, non_coding_transcript_variant
BLK	ENST00000696154.2 linkuse as main transcript	n.274+4510G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.258

AC:

39115

AN:

151576

Hom.:

6363

Cov.:

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

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

1.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over