chr10-94686875-G-A

Variant names:

• chr10-94686875-G-A
• rs1010570
• NM_000772.3:c.169-895G>A

Variant summary

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

The NM_000772.3(CYP2C18):​c.169-895G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,016 control chromosomes in the GnomAD database, including 7,792 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 0.31 (7792 hom., cov: 32)
• Consequence: CYP2C18 NM_000772.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• Publications: 6 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2C18	NM_000772.3	c.169-895G>A		intron_variant	Intron 1 of 8	ENST00000285979.11	NP_000763.1
CYP2C18	NM_001128925.2	c.169-895G>A		intron_variant	Intron 1 of 7		NP_001122397.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2C18	ENST00000285979.11	c.169-895G>A		intron_variant	Intron 1 of 8	1	NM_000772.3	ENSP00000285979.6
CYP2C18	ENST00000339022.6	c.169-895G>A		intron_variant	Intron 1 of 7	1		ENSP00000341293.5

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47224 AN: 151898 Hom.: 7773 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.311 AC: 47283 AN: 152016 Hom.: 7792 Cov.: 32 AF XY: 0.314 AC XY: 23324 AN XY: 74322

African (AFR) AF: 0.405 AC: 16794 AN: 41446

American (AMR) AF: 0.247 AC: 3766 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3464

East Asian (EAS) AF: 0.433 AC: 2234 AN: 5160

South Asian (SAS) AF: 0.471 AC: 2275 AN: 4826

European-Finnish (FIN) AF: 0.265 AC: 2802 AN: 10582

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17500 AN: 67964

Other (OTH) AF: 0.300 AC: 633 AN: 2112

Alfa AF: 0.267 Hom.: 1269

Bravo AF: 0.308

Asia WGS AF: 0.473 AC: 1640 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
DANN	Benign	0.51
PhyloP100		-0.49
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: rs1010570; hg19: chr10-96446632;