chr15-82538321-T-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001021.6(RPS17):āc.312A>Gā(p.Glu104Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00412 in 1,613,404 control chromosomes in the GnomAD database, including 239 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_001021.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPS17 | NM_001021.6 | c.312A>G | p.Glu104Glu | synonymous_variant | Exon 4 of 5 | ENST00000647841.1 | NP_001012.1 | |
RPS17 | NR_111943.2 | n.634A>G | non_coding_transcript_exon_variant | Exon 3 of 4 | ||||
RPS17 | NR_111944.3 | n.341A>G | non_coding_transcript_exon_variant | Exon 4 of 6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPS17 | ENST00000647841.1 | c.312A>G | p.Glu104Glu | synonymous_variant | Exon 4 of 5 | NM_001021.6 | ENSP00000498019.1 | |||
ENSG00000260836 | ENST00000562833.2 | c.1659A>G | p.Glu553Glu | synonymous_variant | Exon 12 of 13 | 3 | ENSP00000454786.2 |
Frequencies
GnomAD3 genomes AF: 0.0221 AC: 3363AN: 152172Hom.: 123 Cov.: 32
GnomAD4 exome AF: 0.00225 AC: 3289AN: 1461114Hom.: 116 Cov.: 31 AF XY: 0.00190 AC XY: 1381AN XY: 726882
GnomAD4 genome AF: 0.0221 AC: 3361AN: 152290Hom.: 123 Cov.: 32 AF XY: 0.0216 AC XY: 1605AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:1
This variant is associated with the following publications: (PMID: 20054847) -
Diamond-Blackfan anemia 4 Benign:1
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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