chr19-6772861-G-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_005428.4(VAV1):āc.54G>Cā(p.Pro18=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 1,613,996 control chromosomes in the GnomAD database, including 13,901 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. P18P) has been classified as Likely benign.
Frequency
Consequence
NM_005428.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VAV1 | NM_005428.4 | c.54G>C | p.Pro18= | synonymous_variant | 1/27 | ENST00000602142.6 | |
VAV1 | NM_001258206.2 | c.54G>C | p.Pro18= | synonymous_variant | 1/26 | ||
VAV1 | NM_001258207.2 | c.54G>C | p.Pro18= | synonymous_variant | 1/26 | ||
VAV1 | XM_005259642.2 | c.54G>C | p.Pro18= | synonymous_variant | 1/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VAV1 | ENST00000602142.6 | c.54G>C | p.Pro18= | synonymous_variant | 1/27 | 1 | NM_005428.4 | P1 | |
VAV1 | ENST00000304076.6 | c.54G>C | p.Pro18= | synonymous_variant | 1/26 | 1 | |||
VAV1 | ENST00000596764.5 | c.54G>C | p.Pro18= | synonymous_variant | 1/26 | 2 |
Frequencies
GnomAD3 genomes AF: 0.104 AC: 15888AN: 152112Hom.: 945 Cov.: 32
GnomAD3 exomes AF: 0.113 AC: 28281AN: 250722Hom.: 2022 AF XY: 0.121 AC XY: 16373AN XY: 135616
GnomAD4 exome AF: 0.127 AC: 185779AN: 1461766Hom.: 12962 Cov.: 34 AF XY: 0.130 AC XY: 94540AN XY: 727202
GnomAD4 genome AF: 0.104 AC: 15877AN: 152230Hom.: 939 Cov.: 32 AF XY: 0.102 AC XY: 7614AN XY: 74428
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
VAV1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 08, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at