12-96280831-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002595.5(CDK17):c.1511G>A(p.Arg504Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000211 in 1,613,780 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002595.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDK17 | NM_002595.5 | c.1511G>A | p.Arg504Gln | missense_variant | Exon 16 of 17 | ENST00000261211.8 | NP_002586.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDK17 | ENST00000261211.8 | c.1511G>A | p.Arg504Gln | missense_variant | Exon 16 of 17 | 1 | NM_002595.5 | ENSP00000261211.3 | ||
CDK17 | ENST00000543119.6 | c.1511G>A | p.Arg504Gln | missense_variant | Exon 16 of 16 | 2 | ENSP00000444459.2 | |||
CDK17 | ENST00000542666.5 | c.1352G>A | p.Arg451Gln | missense_variant | Exon 15 of 15 | 2 | ENSP00000442926.1 |
Frequencies
GnomAD3 genomes AF: 0.000132 AC: 20AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000120 AC: 30AN: 250908Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135654
GnomAD4 exome AF: 0.000220 AC: 321AN: 1461690Hom.: 0 Cov.: 31 AF XY: 0.000205 AC XY: 149AN XY: 727150
GnomAD4 genome AF: 0.000132 AC: 20AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1511G>A (p.R504Q) alteration is located in exon 16 (coding exon 15) of the CDK17 gene. This alteration results from a G to A substitution at nucleotide position 1511, causing the arginine (R) at amino acid position 504 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