NM_000770.3:c.642+151G>T

Variant names:

• chr10-95064649-C-A
• rs11572093
• NM_000770.3:c.642+151G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000770.3(CYP2C8):​c.642+151G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000162 in 618,040 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000016 (0 hom.)
• Consequence: CYP2C8 NM_000770.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 8 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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2C8	NM_000770.3	c.642+151G>T		intron_variant	Intron 4 of 8	ENST00000371270.6	NP_000761.3
CYP2C8	NM_001198853.1	c.432+151G>T		intron_variant	Intron 4 of 8		NP_001185782.1
CYP2C8	NM_001198855.1	c.432+151G>T		intron_variant	Intron 5 of 9		NP_001185784.1
CYP2C8	NM_001198854.1	c.336+151G>T		intron_variant	Intron 3 of 7		NP_001185783.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2C8	ENST00000371270.6	c.642+151G>T		intron_variant	Intron 4 of 8	1	NM_000770.3	ENSP00000360317.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000162 AC: 1 AN: 618040 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 323104

African (AFR) AF: 0.00 AC: 0 AN: 14846

American (AMR) AF: 0.00 AC: 0 AN: 20396

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15864

East Asian (EAS) AF: 0.00 AC: 0 AN: 30576

South Asian (SAS) AF: 0.00 AC: 0 AN: 48588

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 35962

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2298

European-Non Finnish (NFE) AF: 0.00000239 AC: 1 AN: 418576

Other (OTH) AF: 0.00 AC: 0 AN: 30934

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 17433

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.28
PhyloP100		-1.1

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

Other links and lift over

dbSNP: rs11572093; hg19: chr10-96824406;