14-99500849-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_001099402.2(CCNK):c.495A>T(p.Leu165Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0028 in 1,548,782 control chromosomes in the GnomAD database, including 102 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001099402.2 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCNK | NM_001099402.2 | c.495A>T | p.Leu165Leu | synonymous_variant | Exon 5 of 11 | ENST00000389879.9 | NP_001092872.1 | |
CCDC85C | NM_001144995.2 | c.*14397T>A | 3_prime_UTR_variant | Exon 6 of 6 | ENST00000380243.9 | NP_001138467.1 | ||
CCNK | XM_005268154.5 | c.495A>T | p.Leu165Leu | synonymous_variant | Exon 5 of 11 | XP_005268211.1 | ||
CCNK | XM_047431839.1 | c.495A>T | p.Leu165Leu | synonymous_variant | Exon 6 of 12 | XP_047287795.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCNK | ENST00000389879.9 | c.495A>T | p.Leu165Leu | synonymous_variant | Exon 5 of 11 | 5 | NM_001099402.2 | ENSP00000374529.5 | ||
CCDC85C | ENST00000380243 | c.*14397T>A | 3_prime_UTR_variant | Exon 6 of 6 | 5 | NM_001144995.2 | ENSP00000369592.4 |
Frequencies
GnomAD3 genomes AF: 0.00386 AC: 587AN: 152266Hom.: 14 Cov.: 33
GnomAD3 exomes AF: 0.00902 AC: 1464AN: 162368Hom.: 32 AF XY: 0.00741 AC XY: 634AN XY: 85550
GnomAD4 exome AF: 0.00268 AC: 3744AN: 1396398Hom.: 88 Cov.: 27 AF XY: 0.00251 AC XY: 1734AN XY: 689562
GnomAD4 genome AF: 0.00384 AC: 585AN: 152384Hom.: 14 Cov.: 33 AF XY: 0.00452 AC XY: 337AN XY: 74526
ClinVar
Submissions by phenotype
CCNK-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at