X-152135595-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_021048.5(MAGEA10):c.26G>A(p.Arg9His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000967 in 1,137,846 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 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. R9C) has been classified as Uncertain significance.
Frequency
Consequence
NM_021048.5 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 |
---|---|---|---|---|---|---|---|---|
MAGEA10 | NM_021048.5 | c.26G>A | p.Arg9His | missense_variant | Exon 4 of 4 | ENST00000370323.9 | NP_066386.3 | |
MAGEA10 | NM_001011543.3 | c.26G>A | p.Arg9His | missense_variant | Exon 5 of 5 | NP_001011543.3 | ||
MAGEA10 | NM_001251828.2 | c.26G>A | p.Arg9His | missense_variant | Exon 5 of 5 | NP_001238757.2 | ||
LOC100533997 | NM_001204811.3 | c.-278+2880G>A | intron_variant | Intron 1 of 3 | NP_001191740.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000445 AC: 5AN: 112318Hom.: 0 Cov.: 23 AF XY: 0.0000580 AC XY: 2AN XY: 34466
GnomAD4 exome AF: 0.00000585 AC: 6AN: 1025528Hom.: 0 Cov.: 31 AF XY: 0.00000920 AC XY: 3AN XY: 326068
GnomAD4 genome AF: 0.0000445 AC: 5AN: 112318Hom.: 0 Cov.: 23 AF XY: 0.0000580 AC XY: 2AN XY: 34466
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.26G>A (p.R9H) alteration is located in exon 5 (coding exon 1) of the MAGEA10 gene. This alteration results from a G to A substitution at nucleotide position 26, causing the arginine (R) at amino acid position 9 to be replaced by a histidine (H). 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