chr7-39951119-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003718.5(CDK13):āc.478G>Cā(p.Gly160Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000915 in 1,092,704 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ). Synonymous variant affecting the same amino acid position (i.e. G160G) has been classified as Likely benign.
Frequency
Consequence
NM_003718.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDK13 | NM_003718.5 | c.478G>C | p.Gly160Arg | missense_variant | 1/14 | ENST00000181839.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDK13 | ENST00000181839.10 | c.478G>C | p.Gly160Arg | missense_variant | 1/14 | 1 | NM_003718.5 | P3 | |
CDK13 | ENST00000340829.10 | c.478G>C | p.Gly160Arg | missense_variant | 1/14 | 1 | A1 | ||
CDK13 | ENST00000643868.1 | c.103G>C | p.Gly35Arg | missense_variant | 1/1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 9.15e-7 AC: 1AN: 1092704Hom.: 0 Cov.: 33 AF XY: 0.00000193 AC XY: 1AN XY: 517130
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 25, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CDK13 protein function. ClinVar contains an entry for this variant (Variation ID: 521529). This variant has not been reported in the literature in individuals affected with CDK13-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 160 of the CDK13 protein (p.Gly160Arg). - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Oct 21, 2020 | Not observed in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at