10-95037285-C-T

Variant names:

• chr10-95037285-C-T
• NM_000770.3:c.1316G>A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000770.3(CYP2C8):​c.1316G>A​(p.Gly439Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,252 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: CYP2C8 NM_000770.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.543

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2C8	NM_000770.3	c.1316G>A	p.Gly439Glu	missense_variant	Exon 9 of 9	ENST00000371270.6	NP_000761.3
CYP2C8	NM_001198853.1	c.1106G>A	p.Gly369Glu	missense_variant	Exon 9 of 9		NP_001185782.1
CYP2C8	NM_001198855.1	c.1106G>A	p.Gly369Glu	missense_variant	Exon 10 of 10		NP_001185784.1
CYP2C8	NM_001198854.1	c.1010G>A	p.Gly337Glu	missense_variant	Exon 8 of 8		NP_001185783.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2C8	ENST00000371270.6	c.1316G>A	p.Gly439Glu	missense_variant	Exon 9 of 9	1	NM_000770.3	ENSP00000360317.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000205 AC: 3 AN: 1461252 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 726900

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000232

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jan 17, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1316G>A (p.G439E) alteration is located in exon 9 (coding exon 9) of the CYP2C8 gene. This alteration results from a G to A substitution at nucleotide position 1316, causing the glycine (G) at amino acid position 439 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.79
BayesDel_addAF	Benign	-0.022	T
BayesDel_noAF	Benign	-0.27
CADD	Benign	17
DANN	Uncertain	0.99
DEOGEN2	Benign	0.28	.;.;.;T
Eigen	Benign	-0.033
Eigen_PC	Benign	-0.22
FATHMM_MKL	Benign	0.075	N
LIST_S2	Uncertain	0.94	.;D;D;D
M_CAP	Benign	0.0092	T
MetaRNN	Uncertain	0.69	D;D;D;D
MetaSVM	Benign	-0.56	T
MutationAssessor	Uncertain	2.5	.;.;.;M
PrimateAI	Benign	0.32	T
PROVEAN	Pathogenic	-5.4	.;D;.;D
REVEL	Benign	0.26
Sift	Pathogenic	0.0	.;D;.;D
Sift4G	Uncertain	0.0020	D;D;D;D
Polyphen		1.0	.;.;.;D
Vest4		0.38
MutPred		0.74		.;.;.;Loss of methylation at R442 (P = 0.0483);
MVP		0.79
MPC		0.18
ClinPred		0.99	D
GERP RS		1.9
Varity_R		0.85
gMVP		0.18

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-96797042;