rs1555779353
Positions:
- chr20-2652732-AGGGCCTGGGCCT-A
- chr20-2652732-AGGGCCTGGGCCT-AGGGCCT
- chr20-2652732-AGGGCCTGGGCCT-AGGGCCTGGGCCTGGGCCT
- chr20-2652732-AGGGCCTGGGCCT-AGGGCCTGGGCCTGGGCCTGGGCCT
- chr20-2652732-AGGGCCTGGGCCT-AGGGCCTGGGCCTGGGCCTGGGCCTGGGCCT
- chr20-2652732-AGGGCCTGGGCCT-AGGGCCTGGGCCTGGGCCTGGGCCTGGGCCTGGGCCT
- chr20-2652732-AGGGCCTGGGCCT-AGGGCCTGGGCCTGGGCCTGGGCCTGGGCCTGGGCCTGGGCCTGGGCCTGGGCCTGGGCCTGGGCCTGGGCCTGGGCCTGGGCCT
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_006392.4(NOP56):c.3+83_4-85del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000298 in 1,108,360 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000034 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000029 ( 0 hom. )
Consequence
NOP56
NM_006392.4 intron
NM_006392.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.12
Genes affected
NOP56 (HGNC:15911): (NOP56 ribonucleoprotein) Nop56p is a yeast nucleolar protein that is part of a complex with the nucleolar proteins Nop58p and fibrillarin. Nop56p is required for assembly of the 60S ribosomal subunit and is involved in pre-rRNA processing. The protein encoded by this gene is similar in sequence to Nop56p and is also found in the nucleolus. Expansion of a GGCCTG repeat from 3-8 copies to 1500-2500 copies in an intron of this gene results in spinocerebellar ataxia 36. Multiple transcript variants encoding several different isoforms have been found for this gene, but the full-length nature of most of them has not been determined. [provided by RefSeq, Jul 2016]
MIR1292 (HGNC:35364): (microRNA 1292) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
?
High AC in GnomAd4 at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOP56 | NM_006392.4 | c.3+83_4-85del | intron_variant | ENST00000329276.10 | |||
NOP56 | NR_027700.3 | n.32+83_33-85del | intron_variant, non_coding_transcript_variant | ||||
NOP56 | NR_145428.2 | n.32+83_33-85del | intron_variant, non_coding_transcript_variant | ||||
MIR1292 | NR_031699.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOP56 | ENST00000329276.10 | c.3+83_4-85del | intron_variant | 1 | NM_006392.4 | P1 | |||
MIR1292 | ENST00000408135.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000343 AC: 5AN: 145896Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000291 AC: 28AN: 962360Hom.: 0 AF XY: 0.0000292 AC XY: 14AN XY: 480058
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ClinVar
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at