rs2294714
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000983.4(RPL22):c.13-10A>G 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 0.285 in 1,563,072 control chromosomes in the GnomAD database, including 65,572 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 0.33 ( 8589 hom., cov: 33)
Exomes 𝑓: 0.28 ( 56983 hom. )
Consequence
RPL22
NM_000983.4 splice_polypyrimidine_tract, intron
NM_000983.4 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00003427
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.03
Genes affected
RPL22 (HGNC:10315): (ribosomal protein L22) 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 cytoplasmic ribosomal protein that is a component of the 60S subunit. The protein belongs to the L22E family of ribosomal proteins. Its initiating methionine residue is post-translationally removed. The protein can bind specifically to Epstein-Barr virus-encoded RNAs (EBERs) 1 and 2. The mouse protein has been shown to be capable of binding to heparin. Transcript variants utilizing alternative polyA signals exist. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. It was previously thought that this gene mapped to 3q26 and that it was fused to the acute myeloid leukemia 1 (AML1) gene located at 21q22 in some therapy-related myelodysplastic syndrome patients with 3;21 translocations; however, these fusions actually involve a ribosomal protein L22 pseudogene located at 3q26, and this gene actually maps to 1p36.3-p36.2. [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 (BayesDel_noAF=-0.74).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPL22 | NM_000983.4 | c.13-10A>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000234875.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL22 | ENST00000234875.9 | c.13-10A>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000983.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.326 AC: 49468AN: 151898Hom.: 8563 Cov.: 33
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GnomAD3 exomes AF: 0.312 AC: 77373AN: 248234Hom.: 12828 AF XY: 0.304 AC XY: 40856AN XY: 134236
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GnomAD4 exome AF: 0.281 AC: 396087AN: 1411056Hom.: 56983 Cov.: 26 AF XY: 0.280 AC XY: 197061AN XY: 704438
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GnomAD4 genome ? AF: 0.326 AC: 49547AN: 152016Hom.: 8589 Cov.: 33 AF XY: 0.332 AC XY: 24659AN XY: 74306
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at