9-133768444-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_001134398.2(VAV2):c.2587C>T(p.Arg863Trp) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000112 in 1,612,632 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001134398.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VAV2 | NM_001134398.2 | c.2587C>T | p.Arg863Trp | missense_variant, splice_region_variant | 29/30 | ENST00000371850.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VAV2 | ENST00000371850.8 | c.2587C>T | p.Arg863Trp | missense_variant, splice_region_variant | 29/30 | 1 | NM_001134398.2 | A1 | |
VAV2 | ENST00000406606.7 | c.2470C>T | p.Arg824Trp | missense_variant, splice_region_variant | 26/27 | 1 | P4 | ||
VAV2 | ENST00000371851.1 | c.2557C>T | p.Arg853Trp | missense_variant, splice_region_variant | 27/28 | 5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249568Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135082
GnomAD4 exome AF: 0.00000959 AC: 14AN: 1460552Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726638
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74268
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2023 | The c.2587C>T (p.R863W) alteration is located in exon 29 (coding exon 29) of the VAV2 gene. This alteration results from a C to T substitution at nucleotide position 2587, causing the arginine (R) at amino acid position 863 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