rs2233066
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_019066.5(MAGEL2):c.2611G>T(p.Ala871Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00169 in 1,613,756 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A871F) 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.2611G>T | p.Ala871Ser | missense_variant | 1/1 | ENST00000650528.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGEL2 | ENST00000650528.1 | c.2611G>T | p.Ala871Ser | missense_variant | 1/1 | NM_019066.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00904 AC: 1376AN: 152222Hom.: 19 Cov.: 33
GnomAD3 exomes AF: 0.00216 AC: 537AN: 248946Hom.: 4 AF XY: 0.00166 AC XY: 225AN XY: 135180
GnomAD4 exome AF: 0.000926 AC: 1354AN: 1461416Hom.: 17 Cov.: 32 AF XY: 0.000780 AC XY: 567AN XY: 727008
GnomAD4 genome ? AF: 0.00905 AC: 1379AN: 152340Hom.: 19 Cov.: 33 AF XY: 0.00864 AC XY: 644AN XY: 74506
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 15, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 14, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 08, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at