X-151923895-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.231C>T(p.Ser77Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000678 in 1,209,939 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.231C>T | p.Ser77Ser | synonymous_variant | Exon 3 of 3 | ENST00000276344.6 | NP_001011548.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000446 AC: 5AN: 111986Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34148
GnomAD3 exomes AF: 0.0000491 AC: 9AN: 183163Hom.: 0 AF XY: 0.0000296 AC XY: 2AN XY: 67665
GnomAD4 exome AF: 0.0000701 AC: 77AN: 1097953Hom.: 0 Cov.: 36 AF XY: 0.0000660 AC XY: 24AN XY: 363391
GnomAD4 genome AF: 0.0000446 AC: 5AN: 111986Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34148
ClinVar
Submissions by phenotype
not provided Benign:1
MAGEA4: BP4, BP7, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at