14-24097052-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000216780.9(PCK2):c.190G>A(p.Asp64Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00106 in 1,613,702 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000216780.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCK2 | NM_004563.4 | c.190G>A | p.Asp64Asn | missense_variant | 2/10 | ENST00000216780.9 | NP_004554.3 | |
NRL | NM_001354768.3 | c.-27-14177C>T | intron_variant | ENST00000561028.6 | NP_001341697.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCK2 | ENST00000216780.9 | c.190G>A | p.Asp64Asn | missense_variant | 2/10 | 1 | NM_004563.4 | ENSP00000216780 | P1 | |
NRL | ENST00000561028.6 | c.-27-14177C>T | intron_variant | 2 | NM_001354768.3 | ENSP00000454062 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00502 AC: 763AN: 151874Hom.: 8 Cov.: 30
GnomAD3 exomes AF: 0.00146 AC: 366AN: 251338Hom.: 3 AF XY: 0.00113 AC XY: 154AN XY: 135870
GnomAD4 exome AF: 0.000648 AC: 947AN: 1461710Hom.: 11 Cov.: 32 AF XY: 0.000593 AC XY: 431AN XY: 727174
GnomAD4 genome AF: 0.00505 AC: 767AN: 151992Hom.: 8 Cov.: 30 AF XY: 0.00447 AC XY: 332AN XY: 74284
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Sep 18, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 16, 2024 | - - |
PCK2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 26, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at