9-133776056-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001134398.2(VAV2):c.1990C>T(p.Arg664Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000657 in 1,613,024 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R664Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001134398.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VAV2 | NM_001134398.2 | c.1990C>T | p.Arg664Trp | missense_variant | 24/30 | ENST00000371850.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VAV2 | ENST00000371850.8 | c.1990C>T | p.Arg664Trp | missense_variant | 24/30 | 1 | NM_001134398.2 | A1 | |
VAV2 | ENST00000406606.7 | c.1960C>T | p.Arg654Trp | missense_variant | 22/27 | 1 | P4 | ||
VAV2 | ENST00000371851.1 | c.1960C>T | p.Arg654Trp | missense_variant | 22/28 | 5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152244Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000879 AC: 22AN: 250268Hom.: 0 AF XY: 0.0000886 AC XY: 12AN XY: 135496
GnomAD4 exome AF: 0.0000712 AC: 104AN: 1460780Hom.: 0 Cov.: 30 AF XY: 0.0000757 AC XY: 55AN XY: 726704
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152244Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 08, 2024 | The c.1990C>T (p.R664W) alteration is located in exon 24 (coding exon 24) of the VAV2 gene. This alteration results from a C to T substitution at nucleotide position 1990, causing the arginine (R) at amino acid position 664 to be replaced by a tryptophan (W). 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