15-82539981-CCTG-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_001021.6(RPS17):c.152_154delCAG(p.Ala51del) variant causes a disruptive inframe deletion, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001021.6 disruptive_inframe_deletion, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RPS17 | NM_001021.6 | c.152_154delCAG | p.Ala51del | disruptive_inframe_deletion, splice_region_variant | Exon 2 of 5 | ENST00000647841.1 | NP_001012.1 | |
RPS17 | NR_111943.2 | n.474_476delCAG | splice_region_variant, non_coding_transcript_exon_variant | Exon 1 of 4 | ||||
RPS17 | NR_111944.3 | n.181_183delCAG | splice_region_variant, non_coding_transcript_exon_variant | Exon 2 of 6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPS17 | ENST00000647841.1 | c.152_154delCAG | p.Ala51del | disruptive_inframe_deletion, splice_region_variant | Exon 2 of 5 | NM_001021.6 | ENSP00000498019.1 | |||
ENSG00000260836 | ENST00000562833.2 | c.1499_1501delCAG | p.Ala500del | disruptive_inframe_deletion, splice_region_variant | Exon 10 of 13 | 3 | ENSP00000454786.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
Has not been previously published as pathogenic or benign to our knowledge; In-frame deletion of one amino acid in a non-repeat region; Not observed in large population cohorts (Lek et al., 2016); In silico analysis supports a deleterious effect on protein structure/function -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at