chr9-133768447-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001134398.2(VAV2):c.2584G>A(p.Gly862Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000936 in 1,613,040 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar 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 -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VAV2 | ENST00000371850.8 | c.2584G>A | p.Gly862Arg | missense_variant | Exon 29 of 30 | 1 | NM_001134398.2 | ENSP00000360916.3 | ||
VAV2 | ENST00000406606.7 | c.2467G>A | p.Gly823Arg | missense_variant | Exon 26 of 27 | 1 | ENSP00000385362.3 | |||
VAV2 | ENST00000371851.1 | c.2554G>A | p.Gly852Arg | missense_variant | Exon 27 of 28 | 5 | ENSP00000360917.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000560 AC: 14AN: 249864Hom.: 0 AF XY: 0.0000592 AC XY: 8AN XY: 135212
GnomAD4 exome AF: 0.0000986 AC: 144AN: 1460806Hom.: 0 Cov.: 31 AF XY: 0.0000922 AC XY: 67AN XY: 726760
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74428
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2584G>A (p.G862R) 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 2584, causing the glycine (G) at amino acid position 862 to be replaced by an arginine (R). 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