X-151923950-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001011548.1(MAGEA4):c.286C>T(p.Pro96Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000182 in 1,097,440 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P96P) has been classified as Likely benign.
Frequency
Consequence
NM_001011548.1 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGEA4 | NM_001011548.1 | c.286C>T | p.Pro96Ser | missense_variant | Exon 3 of 3 | ENST00000276344.6 | NP_001011548.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.00000549 AC: 1AN: 182256Hom.: 0 AF XY: 0.0000150 AC XY: 1AN XY: 66804
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1097440Hom.: 0 Cov.: 36 AF XY: 0.00000551 AC XY: 2AN XY: 362884
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.286C>T (p.P96S) alteration is located in exon 3 (coding exon 1) of the MAGEA4 gene. This alteration results from a C to T substitution at nucleotide position 286, causing the proline (P) at amino acid position 96 to be replaced by a serine (S). 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