rs176037
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000285879.5(MAGEC1):āc.452C>Gā(p.Thr151Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T151I) has been classified as Likely benign.
Frequency
Consequence
ENST00000285879.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGEC1 | NM_005462.5 | c.452C>G | p.Thr151Ser | missense_variant | 4/4 | ENST00000285879.5 | NP_005453.2 | |
MAGEC1 | XM_011531418.3 | c.452C>G | p.Thr151Ser | missense_variant | 4/4 | XP_011529720.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAGEC1 | ENST00000285879.5 | c.452C>G | p.Thr151Ser | missense_variant | 4/4 | 1 | NM_005462.5 | ENSP00000285879 | P3 | |
MAGEC1 | ENST00000406005.2 | c.-115+309C>G | intron_variant | 1 | ENSP00000385500 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 110064Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 32852 FAILED QC
GnomAD3 exomes AF: 0.00000620 AC: 1AN: 161287Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 60011
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000368 AC: 4AN: 1087465Hom.: 0 Cov.: 52 AF XY: 0.00000553 AC XY: 2AN XY: 361561
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 110116Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 32912
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at