rs191559595
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_019066.5(MAGEL2):āc.383T>Cā(p.Leu128Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00139 in 1,534,806 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGEL2 | NM_019066.5 | c.383T>C | p.Leu128Pro | missense_variant | 1/1 | ENST00000650528.1 | NP_061939.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAGEL2 | ENST00000650528.1 | c.383T>C | p.Leu128Pro | missense_variant | 1/1 | NM_019066.5 | ENSP00000497810.1 |
Frequencies
GnomAD3 genomes AF: 0.00766 AC: 1149AN: 150048Hom.: 13 Cov.: 34
GnomAD3 exomes AF: 0.00162 AC: 228AN: 140536Hom.: 1 AF XY: 0.00122 AC XY: 92AN XY: 75430
GnomAD4 exome AF: 0.000706 AC: 978AN: 1384644Hom.: 8 Cov.: 32 AF XY: 0.000591 AC XY: 404AN XY: 683246
GnomAD4 genome AF: 0.00767 AC: 1151AN: 150162Hom.: 13 Cov.: 34 AF XY: 0.00716 AC XY: 525AN XY: 73368
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 10, 2021 | - - |
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 08, 2014 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 05, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at