rs10509675

Variant names:

• chr10-94729131-G-A
• rs10509675
• NM_000772.3:c.1150-4166G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-94729131-G-A
• chr10-94729131-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000772.3(CYP2C18):​c.1150-4166G>A 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 152,038 control chromosomes in the GnomAD database, including 3,259 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 (3259 hom., cov: 32)
• Consequence: CYP2C18 NM_000772.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• 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 rank	MANE	Protein	UniProt
CYP2C18	NM_000772.3	c.1150-4166G>A		intron_variant	Intron 7 of 8	ENST00000285979.11	NP_000763.1
CYP2C18	NM_001128925.2	c.973-4166G>A		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.1150-4166G>A		intron_variant	Intron 7 of 8	1	NM_000772.3	ENSP00000285979.6
CYP2C18	ENST00000339022.6	c.973-4166G>A		intron_variant	Intron 6 of 7	1		ENSP00000341293.5
ENSG00000276490	ENST00000464755.1	n.790-4166G>A		intron_variant	Intron 5 of 13	2		ENSP00000483243.1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30482 AN: 151920 Hom.: 3258 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.00946

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.228

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: 30484 AN: 152038 Hom.: 3259 Cov.: 32 AF XY: 0.197 AC XY: 14642 AN XY: 74302

African (AFR) AF: 0.224 AC: 9286 AN: 41484

American (AMR) AF: 0.133 AC: 2032 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3472

East Asian (EAS) AF: 0.00948 AC: 49 AN: 5168

South Asian (SAS) AF: 0.162 AC: 781 AN: 4812

European-Finnish (FIN) AF: 0.183 AC: 1938 AN: 10568

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14928 AN: 67958

Other (OTH) AF: 0.199 AC: 422 AN: 2116

Alfa AF: 0.205 Hom.: 4074

Bravo AF: 0.197

Asia WGS AF: 0.0850 AC: 297 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	13
DANN	Benign	0.60
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

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: rs10509675; hg19: chr10-96488888; COSMIC: COSV53672320;