15-82538982-A-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_001021.6(RPS17):āc.159T>Cā(p.Tyr53Tyr) variant causes a synonymous change. The variant allele was found at a frequency of 0.306 in 1,613,126 control chromosomes in the GnomAD database, including 78,142 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001021.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPS17 | NM_001021.6 | c.159T>C | p.Tyr53Tyr | synonymous_variant | Exon 3 of 5 | ENST00000647841.1 | NP_001012.1 | |
RPS17 | NR_111943.2 | n.481T>C | non_coding_transcript_exon_variant | Exon 2 of 4 | ||||
RPS17 | NR_111944.3 | n.188T>C | non_coding_transcript_exon_variant | Exon 3 of 6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPS17 | ENST00000647841.1 | c.159T>C | p.Tyr53Tyr | synonymous_variant | Exon 3 of 5 | NM_001021.6 | ENSP00000498019.1 | |||
ENSG00000260836 | ENST00000562833.2 | c.1506T>C | p.Tyr502Tyr | synonymous_variant | Exon 11 of 13 | 3 | ENSP00000454786.2 |
Frequencies
GnomAD3 genomes AF: 0.264 AC: 40180AN: 151992Hom.: 5747 Cov.: 32
GnomAD4 exome AF: 0.310 AC: 452667AN: 1461016Hom.: 72396 Cov.: 34 AF XY: 0.315 AC XY: 228914AN XY: 726838
GnomAD4 genome AF: 0.264 AC: 40172AN: 152110Hom.: 5746 Cov.: 32 AF XY: 0.267 AC XY: 19847AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.159 T>C (Y53Y) variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. No population data for this variant is available due to low coverage of the RPS17 gene (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This variant occurs at a position that is conserved across species. However, the variant is a synonymous change which does not affect the amino acid sequence, and in silico analysis predicts this variant likely does not affect splicing. In summary, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant. -
Diamond-Blackfan anemia Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at