chr2-70921151-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP3BP4_Moderate
The NM_012476.3(VAX2):c.301C>T(p.Arg101Trp) variant causes a missense change. The variant allele was found at a frequency of 0.000162 in 1,612,876 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R101Q) 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VAX2 | NM_012476.3 | c.301C>T | p.Arg101Trp | missense_variant | 2/3 | ENST00000234392.3 | |
VAX2 | XM_011532750.4 | c.301C>T | p.Arg101Trp | missense_variant | 2/4 | ||
VAX2 | XM_011532751.4 | c.301C>T | p.Arg101Trp | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VAX2 | ENST00000234392.3 | c.301C>T | p.Arg101Trp | missense_variant | 2/3 | 1 | NM_012476.3 | P1 | |
VAX2 | ENST00000432367.6 | c.127C>T | p.Arg43Trp | missense_variant, NMD_transcript_variant | 2/15 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000250 AC: 38AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000313 AC: 78AN: 249278Hom.: 0 AF XY: 0.000356 AC XY: 48AN XY: 134870
GnomAD4 exome AF: 0.000153 AC: 224AN: 1460582Hom.: 0 Cov.: 30 AF XY: 0.000169 AC XY: 123AN XY: 726564
GnomAD4 genome AF: 0.000250 AC: 38AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2022 | The c.301C>T (p.R101W) alteration is located in exon 2 (coding exon 2) of the VAX2 gene. This alteration results from a C to T substitution at nucleotide position 301, causing the arginine (R) at amino acid position 101 to be replaced by a tryptophan (W). 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