15-82540460-G-A
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The 15-82540460-G-A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00103 in 1,586,436 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00079 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 2 hom. )
Consequence
RPS17
NM_001021.6 upstream_gene
NM_001021.6 upstream_gene
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 0.863
Genes affected
RPS17 (HGNC:10397): (ribosomal protein S17) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of four RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S17E family of ribosomal proteins and is located in the cytoplasm. Mutations in this gene cause Diamond-Blackfan anemia 4. Alternative splicing of this gene results in multiple transcript variants. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Apr 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BP6
?
Variant 15-82540460-G-A is Benign according to our data. Variant chr15-82540460-G-A is described in ClinVar as [Benign]. Clinvar id is 1686317.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
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High AC in GnomAd4 at 121 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS17 | NM_001021.6 | upstream_gene_variant | ENST00000647841.1 | ||||
RPS17 | NR_111943.2 | upstream_gene_variant | |||||
RPS17 | NR_111944.3 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS17 | ENST00000647841.1 | upstream_gene_variant | NM_001021.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000802 AC: 122AN: 152144Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000793 AC: 69AN: 86998Hom.: 0 AF XY: 0.000946 AC XY: 44AN XY: 46496
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GnomAD4 exome AF: 0.00106 AC: 1520AN: 1434174Hom.: 2 Cov.: 32 AF XY: 0.00107 AC XY: 759AN XY: 710206
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GnomAD4 genome ? AF: 0.000795 AC: 121AN: 152262Hom.: 0 Cov.: 33 AF XY: 0.000846 AC XY: 63AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at