chr10-94733952-A-G

Position:

• chr10-94733952-A-G

Variant summary

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

The NM_000772.3(CYP2C18):​c.1291+514A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 151,850 control chromosomes in the GnomAD database, including 3,251 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 0.20 (3251 hom., cov: 31)
• Consequence: CYP2C18 NM_000772.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

CYP2C18 (HGNC:2620): (cytochrome P450 family 2 subfamily C member 18) 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 but its specific substrate has not yet been determined. The gene is located within a cluster of cytochrome P450 genes on chromosome 10q24. An additional gene, CYP2C17, was once thought to exist; however, CYP2C17 is now considered an artefact based on a chimera of CYP2C18 and CYP2C19. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP2C18	NM_000772.3	c.1291+514A>G		intron_variant		ENST00000285979.11	NP_000763.1
CYP2C18	NM_001128925.2	c.1114+514A>G		intron_variant			NP_001122397.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP2C18	ENST00000285979.11	c.1291+514A>G		intron_variant		1	NM_000772.3	ENSP00000285979	P1
CYP2C18	ENST00000339022.6	c.1114+514A>G		intron_variant		1		ENSP00000341293

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30458 AN: 151732 Hom.: 3250 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.00947

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.201 AC: 30460 AN: 151850 Hom.: 3251 Cov.: 31 AF XY: 0.197 AC XY: 14621 AN XY: 74188

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.00950

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.200

Alfa AF: 0.208 Hom.: 4400

Bravo AF: 0.197

Asia WGS AF: 0.0850 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.79
DANN	Benign	0.53

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: rs11188067; hg19: chr10-96493709;