10-95037713-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000770.3(CYP2C8):c.1292-404G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 152,040 control chromosomes in the GnomAD database, including 36,575 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).
Frequency
Genomes: 𝑓 0.69 ( 36575 hom., cov: 32)
Consequence
CYP2C8
NM_000770.3 intron
NM_000770.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.88
Publications
14 publications found
Genes affected
CYP2C8 (HGNC:2622): (cytochrome P450 family 2 subfamily C member 8) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum and its expression is induced by phenobarbital. The enzyme is known to metabolize many xenobiotics, including the anticonvulsive drug mephenytoin, benzo(a)pyrene, 7-ethyoxycoumarin, and the anti-cancer drug taxol. This gene is located within a cluster of cytochrome P450 genes on chromosome 10q24. Several transcript variants encoding a few different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYP2C8 | NM_000770.3 | c.1292-404G>A | intron_variant | Intron 8 of 8 | ENST00000371270.6 | NP_000761.3 | ||
CYP2C8 | NM_001198853.1 | c.1082-404G>A | intron_variant | Intron 8 of 8 | NP_001185782.1 | |||
CYP2C8 | NM_001198855.1 | c.1082-404G>A | intron_variant | Intron 9 of 9 | NP_001185784.1 | |||
CYP2C8 | NM_001198854.1 | c.986-404G>A | intron_variant | Intron 7 of 7 | NP_001185783.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.687 AC: 104304AN: 151922Hom.: 36523 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
104304
AN:
151922
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.687 AC: 104405AN: 152040Hom.: 36575 Cov.: 32 AF XY: 0.681 AC XY: 50604AN XY: 74318 show subpopulations
GnomAD4 genome
AF:
AC:
104405
AN:
152040
Hom.:
Cov.:
32
AF XY:
AC XY:
50604
AN XY:
74318
show subpopulations
African (AFR)
AF:
AC:
33473
AN:
41478
American (AMR)
AF:
AC:
8508
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
AC:
2450
AN:
3468
East Asian (EAS)
AF:
AC:
2385
AN:
5172
South Asian (SAS)
AF:
AC:
3225
AN:
4818
European-Finnish (FIN)
AF:
AC:
6495
AN:
10548
Middle Eastern (MID)
AF:
AC:
247
AN:
294
European-Non Finnish (NFE)
AF:
AC:
45458
AN:
67962
Other (OTH)
AF:
AC:
1491
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1641
3281
4922
6562
8203
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2109
AN:
3478
ClinVar
Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Pulmonary disease, chronic obstructive, susceptibility to Other:1
Jul 05, 2022
HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas
Significance:association
Review Status:no assertion criteria provided
Collection Method:research
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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