X-152737054-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001166387.4(MAGEA12):āc.893A>Gā(p.His298Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000579 in 1,209,879 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 30 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001166387.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAGEA12 | NM_001166387.4 | c.893A>G | p.His298Arg | missense_variant | 3/3 | ENST00000393869.8 | |
CSAG4 | NR_073432.1 | n.34-2629A>G | intron_variant, non_coding_transcript_variant | ||||
MAGEA12 | NM_001166386.3 | c.893A>G | p.His298Arg | missense_variant | 3/3 | ||
MAGEA12 | NM_005367.7 | c.893A>G | p.His298Arg | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGEA12 | ENST00000393869.8 | c.893A>G | p.His298Arg | missense_variant | 3/3 | 2 | NM_001166387.4 | P1 | |
MAGEA12 | ENST00000357916.8 | c.893A>G | p.His298Arg | missense_variant | 2/2 | 1 | P1 | ||
MAGEA12 | ENST00000393900.4 | c.893A>G | p.His298Arg | missense_variant | 3/3 | 1 | P1 | ||
CSAG4 | ENST00000361201.8 | n.34-2629A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000448 AC: 5AN: 111707Hom.: 0 Cov.: 23 AF XY: 0.0000590 AC XY: 2AN XY: 33871
GnomAD3 exomes AF: 0.000109 AC: 20AN: 183496Hom.: 0 AF XY: 0.000162 AC XY: 11AN XY: 67928
GnomAD4 exome AF: 0.0000592 AC: 65AN: 1098172Hom.: 0 Cov.: 35 AF XY: 0.0000770 AC XY: 28AN XY: 363558
GnomAD4 genome AF: 0.0000448 AC: 5AN: 111707Hom.: 0 Cov.: 23 AF XY: 0.0000590 AC XY: 2AN XY: 33871
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2023 | The c.893A>G (p.H298R) alteration is located in exon 3 (coding exon 1) of the MAGEA12 gene. This alteration results from a A to G substitution at nucleotide position 893, causing the histidine (H) at amino acid position 298 to be replaced by an arginine (R). 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