rs2901783

Variant names:

• chr10-94693342-A-G
• rs2901783
• NM_000772.3:c.482-1575A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-94693342-A-G
• chr10-94693342-A-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.482-1575A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 151,748 control chromosomes in the GnomAD database, including 5,340 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 0.26 (5340 hom., cov: 32)
• Consequence: CYP2C18 NM_000772.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646
• Publications: 9 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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2C18	NM_000772.3	c.482-1575A>G		intron_variant	Intron 3 of 8	ENST00000285979.11	NP_000763.1
CYP2C18	NM_001128925.2	c.482-1575A>G		intron_variant	Intron 3 of 7		NP_001122397.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2C18	ENST00000285979.11	c.482-1575A>G		intron_variant	Intron 3 of 8	1	NM_000772.3	ENSP00000285979.6
CYP2C18	ENST00000339022.6	c.482-1575A>G		intron_variant	Intron 3 of 7	1		ENSP00000341293.5
ENSG00000276490	ENST00000464755.1	n.122-1575A>G		intron_variant	Intron 1 of 13	2		ENSP00000483243.1

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38995 AN: 151630 Hom.: 5327 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.257 AC: 39046 AN: 151748 Hom.: 5340 Cov.: 32 AF XY: 0.261 AC XY: 19361 AN XY: 74100

African (AFR) AF: 0.322 AC: 13314 AN: 41386

American (AMR) AF: 0.190 AC: 2901 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 752 AN: 3470

East Asian (EAS) AF: 0.410 AC: 2102 AN: 5132

South Asian (SAS) AF: 0.453 AC: 2179 AN: 4814

European-Finnish (FIN) AF: 0.236 AC: 2473 AN: 10500

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14573 AN: 67886

Other (OTH) AF: 0.242 AC: 512 AN: 2114

Alfa AF: 0.230 Hom.: 16196

Bravo AF: 0.251

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.46
PhyloP100		-0.65
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: rs2901783; hg19: chr10-96453099;