rs176048
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005462.5(MAGEC1):c.1401C>A(p.His467Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., 0 hem., cov: 21)
Failed GnomAD Quality Control
Consequence
MAGEC1
NM_005462.5 missense
NM_005462.5 missense
Scores
17
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.303
Genes affected
MAGEC1 (HGNC:6812): (MAGE family member C1) This gene is a member of the melanoma antigen gene (MAGE) family. The proteins of this family are tumor-specific antigens that can be recognized by autologous cytolytic T lymphocytes. This protein contains a large number of unique short repetitive sequences in front of the MAGE-homologous sequence, and therefore is about 800 aa longer than the other MAGE proteins. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.037164897).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAGEC1 | NM_005462.5 | c.1401C>A | p.His467Gln | missense_variant | 4/4 | ENST00000285879.5 | |
MAGEC1 | XM_011531418.3 | c.1401C>A | p.His467Gln | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGEC1 | ENST00000285879.5 | c.1401C>A | p.His467Gln | missense_variant | 4/4 | 1 | NM_005462.5 | P3 | |
MAGEC1 | ENST00000406005.2 | c.-115+1258C>A | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 101413Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 27161 FAILED QC
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GnomAD3 exomes AF: 0.00000550 AC: 1AN: 181674Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67206
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GnomAD4 exome Cov.: 54
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GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 101413Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 27161
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Data not reliable, filtered out with message: AC0
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ExAC
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Gain of solvent accessibility (P = 0.0837);
MVP
ClinPred
T
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at