rs200129390
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001715.3(BLK):c.772+16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,614,026 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
BLK
NM_001715.3 intron
NM_001715.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.32
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 -16 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 8-11555500-C-T is Benign according to our data. Variant chr8-11555500-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 258179.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomAd4 at 18 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BLK | NM_001715.3 | c.772+16C>T | intron_variant | ENST00000259089.9 | |||
LOC105379241 | XR_948956.3 | n.1117+218G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLK | ENST00000259089.9 | c.772+16C>T | intron_variant | 1 | NM_001715.3 | P1 | |||
ENST00000602626.2 | n.622+218G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152178Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000144 AC: 36AN: 250758Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135574
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GnomAD4 exome AF: 0.000113 AC: 165AN: 1461730Hom.: 0 Cov.: 31 AF XY: 0.000117 AC XY: 85AN XY: 727166
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GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152296Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74468
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Maturity-onset diabetes of the young type 11 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Mar 21, 2022 | - - |
Computational scores
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Name
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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