chrX-54810019-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_177433.3(MAGED2):c.343G>C(p.Ala115Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,094,649 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 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. A115V) has been classified as Uncertain significance.
Frequency
Consequence
NM_177433.3 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 |
---|---|---|---|---|---|---|---|
MAGED2 | NM_177433.3 | c.343G>C | p.Ala115Pro | missense_variant | 3/13 | ENST00000375068.6 | |
MAGED2 | NM_014599.6 | c.343G>C | p.Ala115Pro | missense_variant | 3/13 | ||
MAGED2 | NM_201222.3 | c.343G>C | p.Ala115Pro | missense_variant | 3/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGED2 | ENST00000375068.6 | c.343G>C | p.Ala115Pro | missense_variant | 3/13 | 1 | NM_177433.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 21
GnomAD3 exomes AF: 0.00000578 AC: 1AN: 172950Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 58874
GnomAD4 exome AF: 0.00000274 AC: 3AN: 1094649Hom.: 0 Cov.: 34 AF XY: 0.00000277 AC XY: 1AN XY: 360529
GnomAD4 genome ? Cov.: 21
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 09, 2023 | BP4_strong - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at