rs142265745
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_021147.5(CCNO):c.107G>T(p.Arg36Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000412 in 1,456,164 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R36H) has been classified as Likely benign.
Frequency
Consequence
NM_021147.5 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCNO | NM_021147.5 | c.107G>T | p.Arg36Leu | missense_variant | Exon 1 of 3 | ENST00000282572.5 | NP_066970.3 | |
CCNO | NR_125346.2 | n.192G>T | non_coding_transcript_exon_variant | Exon 1 of 3 | ||||
CCNO | NR_125347.2 | n.192G>T | non_coding_transcript_exon_variant | Exon 1 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCNO | ENST00000282572.5 | c.107G>T | p.Arg36Leu | missense_variant | Exon 1 of 3 | 1 | NM_021147.5 | ENSP00000282572.4 | ||
CCNO | ENST00000501463.2 | n.107G>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 1 | ENSP00000422485.1 | ||||
CCNO-DT | ENST00000749853.1 | n.184+184C>A | intron_variant | Intron 1 of 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1456164Hom.: 0 Cov.: 32 AF XY: 0.00000552 AC XY: 4AN XY: 724056 show subpopulations
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at