rs1926711

Variant names:

• chr10-94725020-G-A
• rs1926711
• NM_000772.3:c.1149+487G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-94725020-G-A
• chr10-94725020-G-C
• chr10-94725020-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.1149+487G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 148,338 control chromosomes in the GnomAD database, including 3,489 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 (3489 hom., cov: 32)
• Consequence: CYP2C18 NM_000772.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.12
• Publications: 8 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 (EAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000772.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2C18	NM_000772.3	MANE Select	c.1149+487G>A		intron	N/A	NP_000763.1	P33260-1
	CYP2C18	NM_001128925.2		c.972+487G>A		intron	N/A	NP_001122397.1	P33260-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2C18	ENST00000285979.11	TSL:1 MANE Select	c.1149+487G>A		intron	N/A	ENSP00000285979.6	P33260-1
	CYP2C18	ENST00000339022.6	TSL:1	c.972+487G>A		intron	N/A	ENSP00000341293.5	P33260-2
	ENSG00000276490	ENST00000464755.1	TSL:2	n.789+487G>A		intron	N/A	ENSP00000483243.1	A0A087X0B3

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30164 AN: 148274 Hom.: 3483 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.0942

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.203 AC: 30176 AN: 148338 Hom.: 3489 Cov.: 32 AF XY: 0.208 AC XY: 15010 AN XY: 72282

African (AFR) AF: 0.284 AC: 11565 AN: 40686

American (AMR) AF: 0.145 AC: 2155 AN: 14902

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 458 AN: 3454

East Asian (EAS) AF: 0.376 AC: 1915 AN: 5090

South Asian (SAS) AF: 0.341 AC: 1613 AN: 4730

European-Finnish (FIN) AF: 0.185 AC: 1688 AN: 9136

Middle Eastern (MID) AF: 0.0915 AC: 26 AN: 284

European-Non Finnish (NFE) AF: 0.152 AC: 10221 AN: 67090

Other (OTH) AF: 0.179 AC: 369 AN: 2056

Alfa AF: 0.147 Hom.: 1999

Bravo AF: 0.198

Asia WGS AF: 0.356 AC: 1232 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.24
PhyloP100		-3.1
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: rs1926711; hg19: chr10-96484777;