chr10-95038992-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000770.3(CYP2C8):c.1196A>G(p.Lys399Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,613,204 control chromosomes in the GnomAD database, including 9,719 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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
NM_000770.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2C8 | NM_000770.3 | c.1196A>G | p.Lys399Arg | missense_variant | 8/9 | ENST00000371270.6 | |
CYP2C8 | NM_001198853.1 | c.986A>G | p.Lys329Arg | missense_variant | 8/9 | ||
CYP2C8 | NM_001198855.1 | c.986A>G | p.Lys329Arg | missense_variant | 9/10 | ||
CYP2C8 | NM_001198854.1 | c.890A>G | p.Lys297Arg | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2C8 | ENST00000371270.6 | c.1196A>G | p.Lys399Arg | missense_variant | 8/9 | 1 | NM_000770.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0798 AC: 12149AN: 152168Hom.: 610 Cov.: 32
GnomAD3 exomes AF: 0.0834 AC: 20976AN: 251410Hom.: 1121 AF XY: 0.0850 AC XY: 11545AN XY: 135876
GnomAD4 exome AF: 0.106 AC: 154417AN: 1460918Hom.: 9109 Cov.: 30 AF XY: 0.104 AC XY: 75770AN XY: 726856
GnomAD4 genome ? AF: 0.0798 AC: 12145AN: 152286Hom.: 610 Cov.: 32 AF XY: 0.0791 AC XY: 5892AN XY: 74456
ClinVar
Submissions by phenotype
CYP2C8-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 29, 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). - |
Pulmonary disease, chronic obstructive, susceptibility to Other:1
association, no assertion criteria provided | research | HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas | Jul 05, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at