rs12461099
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001022.4(RPS19):c.172+683T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 152,050 control chromosomes in the GnomAD database, including 15,245 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.42 ( 15245 hom., cov: 32)
Consequence
RPS19
NM_001022.4 intron
NM_001022.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.607
Genes affected
RPS19 (HGNC:10402): (ribosomal protein S19) 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 S19E family of ribosomal proteins. It is located in the cytoplasm. Mutations in this gene cause Diamond-Blackfan anemia (DBA), a constitutional erythroblastopenia characterized by absent or decreased erythroid precursors, in a subset of patients. This suggests a possible extra-ribosomal function for this gene in erythropoietic differentiation and proliferation, in addition to its ribosomal function. Higher expression levels of this gene in some primary colon carcinomas compared to matched normal colon tissues has been observed. 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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (Cadd=1.398).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS19 | NM_001022.4 | c.172+683T>C | intron_variant | ENST00000598742.6 | |||
RPS19 | NM_001321483.2 | c.172+683T>C | intron_variant | ||||
RPS19 | NM_001321484.2 | c.172+683T>C | intron_variant | ||||
RPS19 | NM_001321485.2 | c.185+670T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS19 | ENST00000598742.6 | c.172+683T>C | intron_variant | 1 | NM_001022.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.417 AC: 63412AN: 151930Hom.: 15247 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.417 AC: 63416AN: 152050Hom.: 15245 Cov.: 32 AF XY: 0.422 AC XY: 31392AN XY: 74308
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ClinVar
Not reported inComputational scores
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Name
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Score
Prediction
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at