9-133770407-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001134398.2(VAV2):c.2318C>T(p.Ser773Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,613,952 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VAV2 | NM_001134398.2 | c.2318C>T | p.Ser773Leu | missense_variant | 27/30 | ENST00000371850.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VAV2 | ENST00000371850.8 | c.2318C>T | p.Ser773Leu | missense_variant | 27/30 | 1 | NM_001134398.2 | A1 | |
VAV2 | ENST00000406606.7 | c.2288C>T | p.Ser763Leu | missense_variant | 25/27 | 1 | P4 | ||
VAV2 | ENST00000371851.1 | c.2288C>T | p.Ser763Leu | missense_variant | 25/28 | 5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251278Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135836
GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461748Hom.: 1 Cov.: 32 AF XY: 0.0000261 AC XY: 19AN XY: 727176
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.2318C>T (p.S773L) alteration is located in exon 27 (coding exon 27) of the VAV2 gene. This alteration results from a C to T substitution at nucleotide position 2318, causing the serine (S) at amino acid position 773 to be replaced by a leucine (L). 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