16-29813773-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM1BP4_ModerateBP6BS2_Supporting
The NM_145239.3(PRRT2):c.719G>A(p.Arg240Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000493 in 1,601,306 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_145239.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRRT2 | NM_145239.3 | c.719G>A | p.Arg240Gln | missense_variant | 2/4 | ENST00000358758.12 | NP_660282.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRRT2 | ENST00000358758.12 | c.719G>A | p.Arg240Gln | missense_variant | 2/4 | 1 | NM_145239.3 | ENSP00000351608.7 | ||
ENSG00000280893 | ENST00000609618.2 | n.719G>A | non_coding_transcript_exon_variant | 2/6 | 5 | ENSP00000476774.2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151966Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000209 AC: 5AN: 238956Hom.: 0 AF XY: 0.0000309 AC XY: 4AN XY: 129362
GnomAD4 exome AF: 0.0000511 AC: 74AN: 1449340Hom.: 0 Cov.: 43 AF XY: 0.0000569 AC XY: 41AN XY: 720452
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151966Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74200
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2022 | The c.719G>A (p.R240Q) alteration is located in exon 2 (coding exon 1) of the PRRT2 gene. This alteration results from a G to A substitution at nucleotide position 719, causing the arginine (R) at amino acid position 240 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Episodic kinesigenic dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 01, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 24, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at