rs199772480
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_019066.5(MAGEL2):c.2660G>A(p.Arg887Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000144 in 1,613,912 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R887W) has been classified as Likely benign.
Frequency
Consequence
NM_019066.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAGEL2 | NM_019066.5 | c.2660G>A | p.Arg887Gln | missense_variant | 1/1 | ENST00000650528.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGEL2 | ENST00000650528.1 | c.2660G>A | p.Arg887Gln | missense_variant | 1/1 | NM_019066.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000190 AC: 29AN: 152252Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000209 AC: 52AN: 249360Hom.: 0 AF XY: 0.000251 AC XY: 34AN XY: 135244
GnomAD4 exome AF: 0.000140 AC: 204AN: 1461542Hom.: 0 Cov.: 32 AF XY: 0.000157 AC XY: 114AN XY: 727068
GnomAD4 genome AF: 0.000190 AC: 29AN: 152370Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74508
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 24, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 07, 2023 | - - |
Schaaf-Yang syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Mar 05, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at