rs200127292
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_021147.5(CCNO):c.264G>T(p.Gln88His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000976 in 1,588,732 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_021147.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCNO | NM_021147.5 | c.264G>T | p.Gln88His | missense_variant | 1/3 | ENST00000282572.5 | |
CCNO | NR_125346.2 | n.349G>T | non_coding_transcript_exon_variant | 1/3 | |||
CCNO | NR_125347.2 | n.349G>T | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCNO | ENST00000282572.5 | c.264G>T | p.Gln88His | missense_variant | 1/3 | 1 | NM_021147.5 | P1 | |
CCNO | ENST00000501463.2 | c.264G>T | p.Gln88His | missense_variant, NMD_transcript_variant | 1/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000453 AC: 69AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000164 AC: 33AN: 201146Hom.: 1 AF XY: 0.0000909 AC XY: 10AN XY: 110024
GnomAD4 exome AF: 0.0000592 AC: 85AN: 1436442Hom.: 1 Cov.: 32 AF XY: 0.0000421 AC XY: 30AN XY: 712676
GnomAD4 genome ? AF: 0.000460 AC: 70AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.000443 AC XY: 33AN XY: 74472
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at