NM_183075.3:c.491-5220G>A

Variant names:

• chr4-107939750-G-A
• rs1493131
• NM_183075.3:c.491-5220G>A

Variant summary

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

The NM_183075.3(CYP2U1):​c.491-5220G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,038 control chromosomes in the GnomAD database, including 2,411 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 0.17 (2411 hom., cov: 31)
• Consequence: CYP2U1 NM_183075.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447
• Publications: 13 publications found

Genes affected

CYP2U1 (HGNC:20582): (cytochrome P450 family 2 subfamily U member 1) 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 enzyme is a hydroxylase that metabolizes arachidonic acid, docosahexaenoic acid, and other long chain fatty acids. [provided by RefSeq, Jul 2008]

CYP2U1-AS1 (HGNC:54817): (CYP2U1 and SGMS2 antisense RNA 1)

LOC107986298 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_183075.3. 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
	CYP2U1	NM_183075.3	MANE Select	c.491-5220G>A		intron	N/A	NP_898898.1	Q7Z449-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2U1	ENST00000332884.11	TSL:1 MANE Select	c.491-5220G>A		intron	N/A	ENSP00000333212.6	Q7Z449-1
	CYP2U1	ENST00000508453.1	TSL:1	c.-138+1574G>A		intron	N/A	ENSP00000423667.1	E9PGH5
	CYP2U1	ENST00000908818.1		c.491-5220G>A		intron	N/A	ENSP00000578877.1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25889 AN: 151920 Hom.: 2412 Cov.: 31

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0219

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.170 AC: 25879 AN: 152038 Hom.: 2411 Cov.: 31 AF XY: 0.170 AC XY: 12653 AN XY: 74340

African (AFR) AF: 0.124 AC: 5158 AN: 41452

American (AMR) AF: 0.151 AC: 2299 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 786 AN: 3468

East Asian (EAS) AF: 0.0220 AC: 114 AN: 5184

South Asian (SAS) AF: 0.0680 AC: 327 AN: 4812

European-Finnish (FIN) AF: 0.225 AC: 2376 AN: 10568

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14263 AN: 67964

Other (OTH) AF: 0.183 AC: 386 AN: 2112

Alfa AF: 0.192 Hom.: 9086

Bravo AF: 0.162

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.57
PhyloP100		0.45
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: rs1493131; hg19: chr4-108860906;