chr5-55231426-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_021147.5(CCNO):c.1002G>C(p.Met334Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000116 in 1,614,156 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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.1002G>C | p.Met334Ile | missense_variant | 3/3 | ENST00000282572.5 | |
CCNO | NR_125346.2 | n.1463G>C | non_coding_transcript_exon_variant | 3/3 | |||
CCNO | NR_125347.2 | n.1092G>C | non_coding_transcript_exon_variant | 3/3 | |||
CCNO | NR_125348.1 | n.1066G>C | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCNO | ENST00000282572.5 | c.1002G>C | p.Met334Ile | missense_variant | 3/3 | 1 | NM_021147.5 | P1 | |
CCNO | ENST00000501463.2 | c.*982G>C | 3_prime_UTR_variant, NMD_transcript_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000559 AC: 85AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000171 AC: 43AN: 251368Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135898
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461850Hom.: 0 Cov.: 31 AF XY: 0.0000578 AC XY: 42AN XY: 727232
GnomAD4 genome ? AF: 0.000578 AC: 88AN: 152306Hom.: 0 Cov.: 33 AF XY: 0.000618 AC XY: 46AN XY: 74474
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at