10-117134319-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001112704.2(VAX1):c.694G>T(p.Ala232Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,054,724 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_001112704.2 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 |
---|---|---|---|---|---|---|---|
VAX1 | NM_001112704.2 | c.694G>T | p.Ala232Ser | missense_variant | 3/3 | ENST00000369206.6 | |
VAX1 | NM_199131.3 | c.430-1842G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VAX1 | ENST00000369206.6 | c.694G>T | p.Ala232Ser | missense_variant | 3/3 | 5 | NM_001112704.2 | P1 | |
VAX1 | ENST00000277905.6 | c.430-1842G>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000123 AC: 18AN: 146546Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000330 AC: 3AN: 908178Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 424744
GnomAD4 genome ? AF: 0.000123 AC: 18AN: 146546Hom.: 0 Cov.: 32 AF XY: 0.000154 AC XY: 11AN XY: 71234
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.694G>T (p.A232S) alteration is located in exon 3 (coding exon 3) of the VAX1 gene. This alteration results from a G to T substitution at nucleotide position 694, causing the alanine (A) at amino acid position 232 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 12, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at