19-6772861-G-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005428.4(VAV1):c.54G>T(p.Pro18=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000644 in 1,614,012 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P18P) has been classified as Benign.
Frequency
Consequence
NM_005428.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VAV1 | NM_005428.4 | c.54G>T | p.Pro18= | synonymous_variant | 1/27 | ENST00000602142.6 | |
VAV1 | NM_001258206.2 | c.54G>T | p.Pro18= | synonymous_variant | 1/26 | ||
VAV1 | NM_001258207.2 | c.54G>T | p.Pro18= | synonymous_variant | 1/26 | ||
VAV1 | XM_005259642.2 | c.54G>T | p.Pro18= | synonymous_variant | 1/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VAV1 | ENST00000602142.6 | c.54G>T | p.Pro18= | synonymous_variant | 1/27 | 1 | NM_005428.4 | P1 | |
VAV1 | ENST00000304076.6 | c.54G>T | p.Pro18= | synonymous_variant | 1/26 | 1 | |||
VAV1 | ENST00000596764.5 | c.54G>T | p.Pro18= | synonymous_variant | 1/26 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250722Hom.: 0 AF XY: 0.0000959 AC XY: 13AN XY: 135616
GnomAD4 exome AF: 0.0000499 AC: 73AN: 1461774Hom.: 0 Cov.: 34 AF XY: 0.0000440 AC XY: 32AN XY: 727210
GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at