X-49317256-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001098413.4(GAGE10):āc.296C>Gā(p.Pro99Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00162 in 1,205,729 control chromosomes in the GnomAD database, including 4 homozygotes. There are 577 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001098413.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GAGE10 | NM_001098413.4 | c.296C>G | p.Pro99Arg | missense_variant | 4/5 | ENST00000407599.4 | NP_001091883.3 | |
GAGE10 | XM_024452325.1 | c.254C>G | p.Pro85Arg | missense_variant | 2/3 | XP_024308093.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GAGE10 | ENST00000407599.4 | c.296C>G | p.Pro99Arg | missense_variant | 4/5 | 5 | NM_001098413.4 | ENSP00000385415.3 |
Frequencies
GnomAD3 genomes AF: 0.00105 AC: 117AN: 111324Hom.: 0 Cov.: 22 AF XY: 0.000865 AC XY: 29AN XY: 33524
GnomAD3 exomes AF: 0.000960 AC: 176AN: 183420Hom.: 0 AF XY: 0.000987 AC XY: 67AN XY: 67882
GnomAD4 exome AF: 0.00168 AC: 1841AN: 1094354Hom.: 4 Cov.: 30 AF XY: 0.00152 AC XY: 548AN XY: 360412
GnomAD4 genome AF: 0.00105 AC: 117AN: 111375Hom.: 0 Cov.: 22 AF XY: 0.000863 AC XY: 29AN XY: 33585
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 17, 2024 | The c.296C>G (p.P99R) alteration is located in exon 4 (coding exon 3) of the GAGE10 gene. This alteration results from a C to G substitution at nucleotide position 296, causing the proline (P) at amino acid position 99 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