rs1256517
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000484315.1(RPL36AP2):n.138T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 223,070 control chromosomes in the GnomAD database, including 7,183 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 0.23 ( 6302 hom., cov: 32)
Exomes 𝑓: 0.14 ( 881 hom. )
Consequence
RPL36AP2
ENST00000484315.1 non_coding_transcript_exon
ENST00000484315.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.21
Genes affected
RPL36AP2 (HGNC:19777): (ribosomal protein L36a pseudogene 2)
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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=-0.79).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL36AP2 | ENST00000484315.1 | n.138T>C | non_coding_transcript_exon_variant | 1/1 | |||||
ENST00000555736.1 | n.153-21243A>G | intron_variant, non_coding_transcript_variant | 5 | ||||||
ENST00000553754.1 | n.368+479A>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.227 AC: 34552AN: 151992Hom.: 6276 Cov.: 32
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GnomAD4 exome AF: 0.139 AC: 9841AN: 70960Hom.: 881 Cov.: 0 AF XY: 0.137 AC XY: 5816AN XY: 42440
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GnomAD4 genome ? AF: 0.228 AC: 34622AN: 152110Hom.: 6302 Cov.: 32 AF XY: 0.224 AC XY: 16673AN XY: 74364
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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
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at