rs12845617
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_005462.5(MAGEC1):c.3174G>A(p.Glu1058=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 1,201,785 control chromosomes in the GnomAD database, including 10,033 homozygotes. There are 61,860 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.14 ( 858 hom., 4678 hem., cov: 23)
Exomes 𝑓: 0.16 ( 9175 hom. 57182 hem. )
Consequence
MAGEC1
NM_005462.5 synonymous
NM_005462.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.291
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant X-141908578-G-A is Benign according to our data. Variant chrX-141908578-G-A is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=0.291 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAGEC1 | NM_005462.5 | c.3174G>A | p.Glu1058= | synonymous_variant | 4/4 | ENST00000285879.5 | |
MAGEC1 | XM_011531418.3 | c.3174G>A | p.Glu1058= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGEC1 | ENST00000285879.5 | c.3174G>A | p.Glu1058= | synonymous_variant | 4/4 | 1 | NM_005462.5 | P3 | |
MAGEC1 | ENST00000406005.2 | c.375G>A | p.Glu125= | synonymous_variant | 4/4 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.144 AC: 15917AN: 110857Hom.: 860 Cov.: 23 AF XY: 0.141 AC XY: 4676AN XY: 33127
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GnomAD3 exomes AF: 0.148 AC: 25829AN: 174142Hom.: 1287 AF XY: 0.153 AC XY: 9153AN XY: 59686
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GnomAD4 exome AF: 0.158 AC: 171838AN: 1090876Hom.: 9175 Cov.: 34 AF XY: 0.160 AC XY: 57182AN XY: 357648
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GnomAD4 genome ? AF: 0.144 AC: 15917AN: 110909Hom.: 858 Cov.: 23 AF XY: 0.141 AC XY: 4678AN XY: 33189
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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