rs1341162

Positions:

• chr10-95050855-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000770.3(CYP2C8):​c.820-4904G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 148,616 control chromosomes in the GnomAD database, including 7,639 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (7639 hom., cov: 32)
• Consequence: CYP2C8 NM_000770.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP2C8	NM_000770.3	c.820-4904G>A		intron_variant		ENST00000371270.6	NP_000761.3
CYP2C8	NM_001198853.1	c.610-4904G>A		intron_variant			NP_001185782.1
CYP2C8	NM_001198854.1	c.514-4904G>A		intron_variant			NP_001185783.1
CYP2C8	NM_001198855.1	c.610-4904G>A		intron_variant			NP_001185784.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP2C8	ENST00000371270.6	c.820-4904G>A		intron_variant		1	NM_000770.3	ENSP00000360317	P1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 45210 AN: 148500 Hom.: 7619 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.322

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.305 AC: 45265 AN: 148616 Hom.: 7639 Cov.: 32 AF XY: 0.305 AC XY: 22155 AN XY: 72556

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.327

Alfa AF: 0.267 Hom.: 1311

Bravo AF: 0.304

Asia WGS AF: 0.386 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.25

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1341162; hg19: chr10-96810612;