rs146224183
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_015488.5(PNKD):c.930C>A(p.Ala310=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000377 in 1,593,070 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A310A) has been classified as Benign.
Frequency
Consequence
NM_015488.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNKD | NM_015488.5 | c.930C>A | p.Ala310= | synonymous_variant | 9/10 | ENST00000273077.9 | |
CATIP-AS2 | NR_125777.1 | n.120+6644G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNKD | ENST00000273077.9 | c.930C>A | p.Ala310= | synonymous_variant | 9/10 | 1 | NM_015488.5 | ||
CATIP-AS2 | ENST00000411433.1 | n.120+6644G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152126Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000928 AC: 2AN: 215490Hom.: 0 AF XY: 0.00000862 AC XY: 1AN XY: 115966
GnomAD4 exome AF: 0.00000278 AC: 4AN: 1440944Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 714806
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152126Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74302
ClinVar
Submissions by phenotype
Paroxysmal nonkinesigenic dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 08, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at