chr10-117134369-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001112704.2(VAX1):c.644C>A(p.Pro215Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000141 in 1,204,870 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VAX1 | NM_001112704.2 | c.644C>A | p.Pro215Gln | missense_variant | 3/3 | ENST00000369206.6 | |
VAX1 | NM_199131.3 | c.430-1892C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VAX1 | ENST00000369206.6 | c.644C>A | p.Pro215Gln | missense_variant | 3/3 | 5 | NM_001112704.2 | P1 | |
VAX1 | ENST00000277905.6 | c.430-1892C>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000202 AC: 3AN: 148278Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000133 AC: 14AN: 1056484Hom.: 0 Cov.: 32 AF XY: 0.0000160 AC XY: 8AN XY: 501134
GnomAD4 genome ? AF: 0.0000202 AC: 3AN: 148386Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 1AN XY: 72324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2023 | The c.644C>A (p.P215Q) alteration is located in exon 3 (coding exon 3) of the VAX1 gene. This alteration results from a C to A substitution at nucleotide position 644, causing the proline (P) at amino acid position 215 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