rs12410676
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006113.5(VAV3):c.1846C>T(p.Pro616Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 1,612,830 control chromosomes in the GnomAD database, including 14,511 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_006113.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VAV3 | NM_006113.5 | c.1846C>T | p.Pro616Ser | missense_variant | 20/27 | ENST00000370056.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VAV3 | ENST00000370056.9 | c.1846C>T | p.Pro616Ser | missense_variant | 20/27 | 1 | NM_006113.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.111 AC: 16828AN: 151900Hom.: 1062 Cov.: 32
GnomAD3 exomes AF: 0.137 AC: 34379AN: 250354Hom.: 2715 AF XY: 0.139 AC XY: 18796AN XY: 135278
GnomAD4 exome AF: 0.131 AC: 191521AN: 1460814Hom.: 13447 Cov.: 32 AF XY: 0.133 AC XY: 96355AN XY: 726698
GnomAD4 genome ? AF: 0.111 AC: 16845AN: 152016Hom.: 1064 Cov.: 32 AF XY: 0.112 AC XY: 8304AN XY: 74316
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at