16-18784832-TAAC-T
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001019.5(RPS15A):c.214-12_214-10del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000182 in 1,585,296 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00018 ( 1 hom. )
Consequence
RPS15A
NM_001019.5 splice_polypyrimidine_tract, intron
NM_001019.5 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.303
Genes affected
RPS15A (HGNC:10389): (ribosomal protein S15a) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 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 S8P family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
Variant 16-18784832-TAAC-T is Benign according to our data. Variant chr16-18784832-TAAC-T is described in ClinVar as [Likely_benign]. Clinvar id is 2746992.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 24 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS15A | NM_001019.5 | c.214-12_214-10del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000322989.8 | |||
RPS15A | NM_001030009.2 | c.214-12_214-10del | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS15A | ENST00000322989.8 | c.214-12_214-10del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001019.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152034Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000220 AC: 51AN: 231822Hom.: 1 AF XY: 0.000183 AC XY: 23AN XY: 125518
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GnomAD4 exome AF: 0.000184 AC: 264AN: 1433144Hom.: 1 AF XY: 0.000174 AC XY: 124AN XY: 713444
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GnomAD4 genome AF: 0.000158 AC: 24AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74390
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 20, 2023 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at