X-152135220-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_021048.5(MAGEA10):c.401T>A(p.Ile134Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I134T) has been classified as Likely benign.
Frequency
Consequence
NM_021048.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGEA10 | NM_021048.5 | c.401T>A | p.Ile134Lys | missense_variant | Exon 4 of 4 | ENST00000370323.9 | NP_066386.3 | |
MAGEA10 | NM_001011543.3 | c.401T>A | p.Ile134Lys | missense_variant | Exon 5 of 5 | NP_001011543.3 | ||
MAGEA10 | NM_001251828.2 | c.401T>A | p.Ile134Lys | missense_variant | Exon 5 of 5 | NP_001238757.2 | ||
LOC100533997 | NM_001204811.3 | c.-278+3255T>A | intron_variant | Intron 1 of 3 | NP_001191740.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 exomes AF: 0.00000552 AC: 1AN: 181113Hom.: 0 AF XY: 0.0000152 AC XY: 1AN XY: 65665
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 9.12e-7 AC: 1AN: 1096334Hom.: 0 Cov.: 32 AF XY: 0.00000276 AC XY: 1AN XY: 361840
GnomAD4 genome Cov.: 22
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at