X-135906491-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_001381902.1(SAGE1):c.676C>T(p.Arg226*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000745 in 1,208,593 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. Variant has been reported in ClinVar as not provided (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001381902.1 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAGE1 | NM_001381902.1 | c.676C>T | p.Arg226* | stop_gained | Exon 7 of 20 | ENST00000370709.4 | NP_001368831.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000888 AC: 1AN: 112567Hom.: 0 Cov.: 29 AF XY: 0.0000288 AC XY: 1AN XY: 34719
GnomAD3 exomes AF: 0.00000547 AC: 1AN: 182775Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67281
GnomAD4 exome AF: 0.00000730 AC: 8AN: 1096026Hom.: 0 Cov.: 30 AF XY: 0.00000277 AC XY: 1AN XY: 361452
GnomAD4 genome AF: 0.00000888 AC: 1AN: 112567Hom.: 0 Cov.: 29 AF XY: 0.0000288 AC XY: 1AN XY: 34719
ClinVar
Submissions by phenotype
not provided Other:1
Variant classified as Uncertain significance and reported on 02-14-2020 by Macrogen. GenomeConnect-Association for Creatine Deficiencies assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at