10-94735727-G-A

Variant names:

• chr10-94735727-G-A
• rs1042194
• NM_000772.3:c.*283G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000772.3(CYP2C18):​c.*283G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000005 in 200,156 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000050 (0 hom.)
• Consequence: CYP2C18 NM_000772.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• Publications: 18 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2C18	NM_000772.3	MANE Select	c.*283G>A		3_prime_UTR	Exon 9 of 9	NP_000763.1
	CYP2C18	NM_001128925.2		c.*283G>A		3_prime_UTR	Exon 8 of 8	NP_001122397.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2C18	ENST00000285979.11	TSL:1 MANE Select	c.*283G>A		3_prime_UTR	Exon 9 of 9	ENSP00000285979.6
	ENSG00000276490	ENST00000464755.1	TSL:2	n.931+2289G>A		intron	N/A	ENSP00000483243.1
	CYP2C18	ENST00000339022.6	TSL:1	c.*283G>A		downstream_gene	N/A	ENSP00000341293.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000500 AC: 1 AN: 200156 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 101526

African (AFR) AF: 0.00 AC: 0 AN: 7294

American (AMR) AF: 0.00 AC: 0 AN: 8006

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7200

East Asian (EAS) AF: 0.00 AC: 0 AN: 17692

South Asian (SAS) AF: 0.00 AC: 0 AN: 7014

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12572

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 956

European-Non Finnish (NFE) AF: 0.00000792 AC: 1 AN: 126190

Other (OTH) AF: 0.00 AC: 0 AN: 13232

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.74
PhyloP100		0.25

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: rs1042194; hg19: chr10-96495484;