X-30235947-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002365.5(MAGEB3):c.23C>T(p.Thr8Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00012 in 1,204,830 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 45 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T8A) has been classified as Uncertain significance.
Frequency
Consequence
NM_002365.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGEB3 | NM_002365.5 | c.23C>T | p.Thr8Met | missense_variant | Exon 5 of 5 | ENST00000361644.4 | NP_002356.2 | |
MAGEB3 | NM_001386865.1 | c.23C>T | p.Thr8Met | missense_variant | Exon 3 of 3 | NP_001373794.1 | ||
MAGEB3 | XM_011545513.3 | c.23C>T | p.Thr8Met | missense_variant | Exon 4 of 4 | XP_011543815.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000126 AC: 14AN: 111350Hom.: 0 Cov.: 22 AF XY: 0.000179 AC XY: 6AN XY: 33536
GnomAD3 exomes AF: 0.000120 AC: 21AN: 175066Hom.: 0 AF XY: 0.0000995 AC XY: 6AN XY: 60276
GnomAD4 exome AF: 0.000120 AC: 131AN: 1093480Hom.: 0 Cov.: 30 AF XY: 0.000108 AC XY: 39AN XY: 359622
GnomAD4 genome AF: 0.000126 AC: 14AN: 111350Hom.: 0 Cov.: 22 AF XY: 0.000179 AC XY: 6AN XY: 33536
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.23C>T (p.T8M) alteration is located in exon 5 (coding exon 1) of the MAGEB3 gene. This alteration results from a C to T substitution at nucleotide position 23, causing the threonine (T) at amino acid position 8 to be replaced by a methionine (M). 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