rs757880754
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000513620.1(NRBF2P6):n.273dup 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 0.0000045 in 1,556,426 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000043 ( 0 hom. )
Consequence
NRBF2P6
ENST00000513620.1 non_coding_transcript_exon
ENST00000513620.1 non_coding_transcript_exon
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.395
Genes affected
DIS3L2 (HGNC:28648): (DIS3 like 3'-5' exoribonuclease 2) The protein encoded by this gene is similar in sequence to 3'/5' exonucleolytic subunits of the RNA exosome. The exosome is a large multimeric ribonucleotide complex responsible for degrading various RNA substrates. Several transcript variants, some protein-coding and some not, have been found for this gene. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DIS3L2 | NM_001257281.2 | c.1625dup | p.His542GlnfsTer6 | frameshift_variant | 14/14 | NP_001244210.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NRBF2P6 | ENST00000513620.1 | n.273dup | non_coding_transcript_exon_variant | 1/1 | ||||||
DIS3L2 | ENST00000273009.10 | c.1625dup | p.His542GlnfsTer6 | frameshift_variant | 14/14 | 2 | ENSP00000273009 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000619 AC: 1AN: 161454Hom.: 0 AF XY: 0.0000116 AC XY: 1AN XY: 86432
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GnomAD4 exome AF: 0.00000427 AC: 6AN: 1404224Hom.: 0 Cov.: 30 AF XY: 0.00000577 AC XY: 4AN XY: 693152
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74356
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, no assertion criteria provided | research | Gharavi Laboratory, Columbia University | Sep 16, 2018 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at