chr2-178432137-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003690.5(PRKRA):āc.902A>Gā(p.Asn301Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,614,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_003690.5 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 |
---|---|---|---|---|---|---|---|
PRKRA | NM_003690.5 | c.902A>G | p.Asn301Ser | missense_variant | 8/8 | ENST00000325748.9 | |
CHROMR | NR_110204.1 | n.872-1245T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKRA | ENST00000325748.9 | c.902A>G | p.Asn301Ser | missense_variant | 8/8 | 1 | NM_003690.5 | P1 | |
CHROMR | ENST00000453026.7 | n.896-1245T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152254Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251396Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135882
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461878Hom.: 0 Cov.: 57 AF XY: 0.0000316 AC XY: 23AN XY: 727236
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152254Hom.: 0 Cov.: 35 AF XY: 0.0000134 AC XY: 1AN XY: 74390
ClinVar
Submissions by phenotype
Dystonia 16 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 29, 2020 | 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with PRKRA-related conditions. This variant is present in population databases (rs778511975, ExAC 0.01%). This sequence change replaces asparagine with serine at codon 301 of the PRKRA protein (p.Asn301Ser). The asparagine residue is moderately conserved and there is a small physicochemical difference between asparagine and serine. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at