rs11237429
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_080491.3(GAB2):c.377-29T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00361 in 1,603,300 control chromosomes in the GnomAD database, including 193 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 0.019 ( 107 hom., cov: 31)
Exomes 𝑓: 0.0020 ( 86 hom. )
Consequence
GAB2
NM_080491.3 intron
NM_080491.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.547
Genes affected
GAB2 (HGNC:14458): (GRB2 associated binding protein 2) This gene is a member of the GRB2-associated binding protein (GAB) gene family. These proteins contain pleckstrin homology (PH) domain, and bind SHP2 tyrosine phosphatase and GRB2 adapter protein. They act as adapters for transmitting various signals in response to stimuli through cytokine and growth factor receptors, and T- and B-cell antigen receptors. The protein encoded by this gene is the principal activator of phosphatidylinositol-3 kinase in response to activation of the high affinity IgE receptor. Two alternatively spliced transcripts encoding different isoforms have been described for this gene. [provided by RefSeq, Nov 2009]
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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=-0.85).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0671 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GAB2 | NM_080491.3 | c.377-29T>C | intron_variant | ENST00000361507.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAB2 | ENST00000361507.5 | c.377-29T>C | intron_variant | 1 | NM_080491.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0194 AC: 2944AN: 152082Hom.: 106 Cov.: 31
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GnomAD3 exomes AF: 0.00527 AC: 1317AN: 250118Hom.: 51 AF XY: 0.00395 AC XY: 535AN XY: 135298
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GnomAD4 exome AF: 0.00195 AC: 2833AN: 1451100Hom.: 86 Cov.: 28 AF XY: 0.00168 AC XY: 1216AN XY: 722268
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GnomAD4 genome ? AF: 0.0194 AC: 2959AN: 152200Hom.: 107 Cov.: 31 AF XY: 0.0187 AC XY: 1391AN XY: 74434
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at