10-94728712-C-T

Variant names:

• chr10-94728712-C-T
• rs932809
• NM_000772.3:c.1149+4179C>T

Variant summary

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

The NM_000772.3(CYP2C18):​c.1149+4179C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 479,746 control chromosomes in the GnomAD database, including 6,443 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 0.17 (2505 hom., cov: 32)
  • Exomes 𝑓: 0.15 (3938 hom.)
• Consequence: CYP2C18 NM_000772.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950

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]

ENSG00000276490 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2C18	NM_000772.3	c.1149+4179C>T		intron_variant	Intron 7 of 8	ENST00000285979.11	NP_000763.1
CYP2C18	NM_001128925.2	c.972+4179C>T		intron_variant	Intron 6 of 7		NP_001122397.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2C18	ENST00000285979.11	c.1149+4179C>T		intron_variant	Intron 7 of 8	1	NM_000772.3	ENSP00000285979.6
CYP2C18	ENST00000339022.6	c.972+4179C>T		intron_variant	Intron 6 of 7	1		ENSP00000341293.5
ENSG00000276490	ENST00000464755.1	n.789+4179C>T		intron_variant	Intron 5 of 13	2		ENSP00000483243.1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26221 AN: 151606 Hom.: 2500 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.153

GnomAD4 exome AF: 0.146 AC: 47989 AN: 328024 Hom.: 3938 AF XY: 0.147 AC XY: 22965 AN XY: 156014

Gnomad4 AFR exome AF: 0.199

Gnomad4 AMR exome AF: 0.0901

Gnomad4 ASJ exome AF: 0.124

Gnomad4 EAS exome AF: 0.289

Gnomad4 SAS exome AF: 0.310

Gnomad4 FIN exome AF: 0.113

Gnomad4 NFE exome AF: 0.141

Gnomad4 OTH exome AF: 0.164

GnomAD4 genome AF: 0.173 AC: 26243 AN: 151722 Hom.: 2505 Cov.: 32 AF XY: 0.177 AC XY: 13119 AN XY: 74134

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.157

Alfa AF: 0.152 Hom.: 1704

Bravo AF: 0.167

Asia WGS AF: 0.305 AC: 1055 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.31

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: rs932809; hg19: chr10-96488469;