rs7824640
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001715.3(BLK):c.176-484G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,182 control chromosomes in the GnomAD database, including 15,986 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 0.45 ( 15986 hom., cov: 34)
Consequence
BLK
NM_001715.3 intron
NM_001715.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.904
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=-0.82).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BLK | NM_001715.3 | c.176-484G>A | intron_variant | ENST00000259089.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLK | ENST00000259089.9 | c.176-484G>A | intron_variant | 1 | NM_001715.3 | P1 | |||
BLK | ENST00000533828.1 | n.374-484G>A | intron_variant, non_coding_transcript_variant | 4 | |||||
BLK | ENST00000645242.1 | n.327-484G>A | intron_variant, non_coding_transcript_variant | ||||||
BLK | ENST00000696154.2 | n.327-484G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.447 AC: 68027AN: 152064Hom.: 15987 Cov.: 34
GnomAD3 genomes
?
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34
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.447 AC: 68055AN: 152182Hom.: 15986 Cov.: 34 AF XY: 0.440 AC XY: 32776AN XY: 74410
GnomAD4 genome
?
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68055
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34
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32776
AN XY:
74410
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916
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at