rs111759069
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_019066.5(MAGEL2):c.1079C>T(p.Ala360Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0098 in 1,504,542 control chromosomes in the GnomAD database, including 114 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A360A) 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 -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAGEL2 | NM_019066.5 | c.1079C>T | p.Ala360Val | missense_variant | 1/1 | ENST00000650528.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGEL2 | ENST00000650528.1 | c.1079C>T | p.Ala360Val | missense_variant | 1/1 | NM_019066.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00692 AC: 1053AN: 152070Hom.: 7 Cov.: 33
GnomAD3 exomes AF: 0.00570 AC: 642AN: 112578Hom.: 3 AF XY: 0.00581 AC XY: 346AN XY: 59508
GnomAD4 exome AF: 0.0101 AC: 13691AN: 1352354Hom.: 107 Cov.: 32 AF XY: 0.00986 AC XY: 6540AN XY: 663390
GnomAD4 genome ? AF: 0.00691 AC: 1052AN: 152188Hom.: 7 Cov.: 33 AF XY: 0.00609 AC XY: 453AN XY: 74386
ClinVar
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 19, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | MAGEL2: BS1, BS2 - |
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 13, 2017 | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 29, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at