chr19-6772851-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP2BP4
The NM_005428.4(VAV1):c.44G>A(p.Arg15Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,461,744 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. R15R) has been classified as Likely benign.
Frequency
Consequence
NM_005428.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VAV1 | NM_005428.4 | c.44G>A | p.Arg15Gln | missense_variant | 1/27 | ENST00000602142.6 | |
VAV1 | NM_001258206.2 | c.44G>A | p.Arg15Gln | missense_variant | 1/26 | ||
VAV1 | NM_001258207.2 | c.44G>A | p.Arg15Gln | missense_variant | 1/26 | ||
VAV1 | XM_005259642.2 | c.44G>A | p.Arg15Gln | missense_variant | 1/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VAV1 | ENST00000602142.6 | c.44G>A | p.Arg15Gln | missense_variant | 1/27 | 1 | NM_005428.4 | P1 | |
VAV1 | ENST00000304076.6 | c.44G>A | p.Arg15Gln | missense_variant | 1/26 | 1 | |||
VAV1 | ENST00000596764.5 | c.44G>A | p.Arg15Gln | missense_variant | 1/26 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250596Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135542
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461744Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 727186
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Feb 10, 2022 | This variant has not been reported in the literature in individuals affected with VAV1-related conditions. This variant is present in population databases (rs373948131, gnomAD 0.002%). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 15 of the VAV1 protein (p.Arg15Gln). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at