15-23644726-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_019066.5(MAGEL2):āc.3017C>Gā(p.Thr1006Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00454 in 1,613,800 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/16 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 | UniProt |
---|---|---|---|---|---|---|---|
MAGEL2 | NM_019066.5 | c.3017C>G | p.Thr1006Ser | missense_variant | 1/1 | ENST00000650528.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGEL2 | ENST00000650528.1 | c.3017C>G | p.Thr1006Ser | missense_variant | 1/1 | NM_019066.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00338 AC: 514AN: 152126Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00334 AC: 832AN: 249152Hom.: 2 AF XY: 0.00320 AC XY: 433AN XY: 135188
GnomAD4 exome AF: 0.00466 AC: 6817AN: 1461556Hom.: 21 Cov.: 32 AF XY: 0.00452 AC XY: 3287AN XY: 727064
GnomAD4 genome AF: 0.00338 AC: 514AN: 152244Hom.: 2 Cov.: 32 AF XY: 0.00322 AC XY: 240AN XY: 74444
ClinVar
Submissions by phenotype
not provided Benign:6
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | MAGEL2: BP4, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 17, 2021 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Nov 11, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
not specified Benign:4
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 27, 2014 | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 02, 2015 | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Prader-Willi syndrome;C5575066:Schaaf-Yang syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at