chrX-152737041-A-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001166387.4(MAGEA12):c.880A>T(p.Ser294Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000014 in 1,210,048 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 7/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001166387.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAGEA12 | NM_001166387.4 | c.880A>T | p.Ser294Cys | missense_variant | 3/3 | ENST00000393869.8 | |
CSAG4 | NR_073432.1 | n.34-2642A>T | intron_variant, non_coding_transcript_variant | ||||
MAGEA12 | NM_001166386.3 | c.880A>T | p.Ser294Cys | missense_variant | 3/3 | ||
MAGEA12 | NM_005367.7 | c.880A>T | p.Ser294Cys | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGEA12 | ENST00000393869.8 | c.880A>T | p.Ser294Cys | missense_variant | 3/3 | 2 | NM_001166387.4 | P1 | |
MAGEA12 | ENST00000357916.8 | c.880A>T | p.Ser294Cys | missense_variant | 2/2 | 1 | P1 | ||
MAGEA12 | ENST00000393900.4 | c.880A>T | p.Ser294Cys | missense_variant | 3/3 | 1 | P1 | ||
CSAG4 | ENST00000361201.8 | n.34-2642A>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000447 AC: 5AN: 111878Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34036
GnomAD3 exomes AF: 0.0000327 AC: 6AN: 183427Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67869
GnomAD4 exome AF: 0.0000109 AC: 12AN: 1098170Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 4AN XY: 363564
GnomAD4 genome AF: 0.0000447 AC: 5AN: 111878Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34036
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.880A>T (p.S294C) alteration is located in exon 3 (coding exon 1) of the MAGEA12 gene. This alteration results from a A to T substitution at nucleotide position 880, causing the serine (S) at amino acid position 294 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at