22-46691699-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_022766.6(CERK):c.1205G>A(p.Arg402Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000682 in 1,613,816 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R402W) has been classified as Uncertain significance.
Frequency
Consequence
NM_022766.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CERK | NM_022766.6 | c.1205G>A | p.Arg402Gln | missense_variant | 11/13 | ENST00000216264.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CERK | ENST00000216264.13 | c.1205G>A | p.Arg402Gln | missense_variant | 11/13 | 1 | NM_022766.6 | P1 | |
CERK | ENST00000443629.5 | c.*583G>A | 3_prime_UTR_variant, NMD_transcript_variant | 10/12 | 1 | ||||
CERK | ENST00000471929.1 | n.294G>A | non_coding_transcript_exon_variant | 3/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250974Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135812
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461670Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727126
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.1205G>A (p.R402Q) alteration is located in exon 11 (coding exon 11) of the CERK gene. This alteration results from a G to A substitution at nucleotide position 1205, causing the arginine (R) at amino acid position 402 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at