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GeneBe

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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0750

Links

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
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
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.

Other links and lift over

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