rs993057859
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_019066.5(MAGEL2):āc.789T>Cā(p.Pro263=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000911 in 1,536,668 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P263P) has been classified as Likely benign.
Frequency
Consequence
NM_019066.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAGEL2 | NM_019066.5 | c.789T>C | p.Pro263= | synonymous_variant | 1/1 | ENST00000650528.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGEL2 | ENST00000650528.1 | c.789T>C | p.Pro263= | synonymous_variant | 1/1 | NM_019066.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152042Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000142 AC: 2AN: 141130Hom.: 0 AF XY: 0.0000132 AC XY: 1AN XY: 75676
GnomAD4 exome AF: 0.00000867 AC: 12AN: 1384626Hom.: 0 Cov.: 32 AF XY: 0.00000878 AC XY: 6AN XY: 683262
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152042Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74262
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 20, 2023 | This sequence change affects codon 263 of the MAGEL2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the MAGEL2 protein. This variant is present in population databases (no rsID available, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with MAGEL2-related conditions. ClinVar contains an entry for this variant (Variation ID: 435796). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 21, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at