chr9-133768584-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001134398.2(VAV2):c.2447G>A(p.Arg816His) variant causes a missense change. The variant allele was found at a frequency of 0.0000861 in 1,613,772 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 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 -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VAV2 | ENST00000371850.8 | c.2447G>A | p.Arg816His | missense_variant | Exon 29 of 30 | 1 | NM_001134398.2 | ENSP00000360916.3 | ||
VAV2 | ENST00000406606.7 | c.2330G>A | p.Arg777His | missense_variant | Exon 26 of 27 | 1 | ENSP00000385362.3 | |||
VAV2 | ENST00000371851.1 | c.2417G>A | p.Arg806His | missense_variant | Exon 27 of 28 | 5 | ENSP00000360917.1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152082Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000957 AC: 24AN: 250654Hom.: 0 AF XY: 0.0000812 AC XY: 11AN XY: 135540
GnomAD4 exome AF: 0.0000869 AC: 127AN: 1461572Hom.: 1 Cov.: 31 AF XY: 0.0000839 AC XY: 61AN XY: 727120
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74394
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2447G>A (p.R816H) 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 2447, causing the arginine (R) at amino acid position 816 to be replaced by a histidine (H). 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