chr9-133768518-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001134398.2(VAV2):c.2513G>A(p.Arg838Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000615 in 1,613,926 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R838W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001134398.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VAV2 | ENST00000371850.8 | c.2513G>A | p.Arg838Gln | missense_variant | Exon 29 of 30 | 1 | NM_001134398.2 | ENSP00000360916.3 | ||
VAV2 | ENST00000406606.7 | c.2396G>A | p.Arg799Gln | missense_variant | Exon 26 of 27 | 1 | ENSP00000385362.3 | |||
VAV2 | ENST00000371851.1 | c.2483G>A | p.Arg828Gln | missense_variant | Exon 27 of 28 | 5 | ENSP00000360917.1 |
Frequencies
GnomAD3 genomes AF: 0.000394 AC: 60AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000294 AC: 74AN: 251344Hom.: 0 AF XY: 0.000309 AC XY: 42AN XY: 135872
GnomAD4 exome AF: 0.000638 AC: 932AN: 1461804Hom.: 0 Cov.: 31 AF XY: 0.000611 AC XY: 444AN XY: 727206
GnomAD4 genome AF: 0.000394 AC: 60AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.000350 AC XY: 26AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2513G>A (p.R838Q) alteration is located in exon 29 (coding exon 29) of the VAV2 gene. This alteration results from a G to A substitution at nucleotide position 2513, causing the arginine (R) at amino acid position 838 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at