2-70933023-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012476.3(VAX2):c.692C>A(p.Pro231Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00001 in 1,598,074 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P231A) has been classified as Uncertain significance.
Frequency
Consequence
NM_012476.3 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 |
---|---|---|---|---|---|---|---|
VAX2 | NM_012476.3 | c.692C>A | p.Pro231Gln | missense_variant | 3/3 | ENST00000234392.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VAX2 | ENST00000234392.3 | c.692C>A | p.Pro231Gln | missense_variant | 3/3 | 1 | NM_012476.3 | P1 | |
VAX2 | ENST00000432367.6 | c.*45+8685C>A | intron_variant, NMD_transcript_variant | 5 | |||||
VAX2 | ENST00000646783.1 | c.80-6395C>A | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152188Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000846 AC: 2AN: 236272Hom.: 0 AF XY: 0.0000156 AC XY: 2AN XY: 127936
GnomAD4 exome AF: 0.00000899 AC: 13AN: 1445886Hom.: 0 Cov.: 32 AF XY: 0.0000125 AC XY: 9AN XY: 717766
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152188Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 27, 2023 | The c.692C>A (p.P231Q) alteration is located in exon 3 (coding exon 3) of the VAX2 gene. This alteration results from a C to A substitution at nucleotide position 692, causing the proline (P) at amino acid position 231 to be replaced by a glutamine (Q). 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