2-218344925-C-T
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 1P and 6B. PP3BP4BP6BS2
The NM_015488.5(PNKD):c.1102C>T(p.Arg368Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000582 in 1,614,004 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R368G) has been classified as Uncertain significance.
Frequency
Consequence
NM_015488.5 missense
Scores
Clinical Significance
Conservation
Publications
Genome browser will be placed here
ACMG classification
Our verdict: Likely_benign. The variant received -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PNKD | NM_015488.5 | c.1102C>T | p.Arg368Trp | missense_variant | Exon 10 of 10 | ENST00000273077.9 | NP_056303.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152178Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000722 AC: 18AN: 249452 AF XY: 0.0000517 show subpopulations
GnomAD4 exome AF: 0.0000616 AC: 90AN: 1461708Hom.: 0 Cov.: 33 AF XY: 0.0000550 AC XY: 40AN XY: 727162 show subpopulations
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152296Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74472 show subpopulations
ClinVar
Submissions by phenotype
Paroxysmal nonkinesigenic dyskinesia 1 Uncertain:1
- -
Paroxysmal nonkinesigenic dyskinesia Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at