X-151924132-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001011548.1(MAGEA4):c.468C>T(p.Ser156Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000686 in 1,210,600 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 25 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001011548.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGEA4 | NM_001011548.1 | c.468C>T | p.Ser156Ser | synonymous_variant | Exon 3 of 3 | ENST00000276344.6 | NP_001011548.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000178 AC: 2AN: 112358Hom.: 0 Cov.: 23 AF XY: 0.0000290 AC XY: 1AN XY: 34522
GnomAD3 exomes AF: 0.0000327 AC: 6AN: 183468Hom.: 0 AF XY: 0.0000294 AC XY: 2AN XY: 67914
GnomAD4 exome AF: 0.0000738 AC: 81AN: 1098187Hom.: 0 Cov.: 36 AF XY: 0.0000660 AC XY: 24AN XY: 363551
GnomAD4 genome AF: 0.0000178 AC: 2AN: 112413Hom.: 0 Cov.: 23 AF XY: 0.0000289 AC XY: 1AN XY: 34587
ClinVar
Submissions by phenotype
not provided Benign:1
MAGEA4: BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at