rs1493131

Positions:

• chr4-107939750-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP2U1	NM_183075.3	c.491-5220G>A		intron_variant		ENST00000332884.11
LOC107986298	XR_001741784.2	n.205-29201C>T		intron_variant, non_coding_transcript_variant
CYP2U1	XM_005262717.2	c.545-5220G>A		intron_variant
CYP2U1	XM_005262720.2	c.490+7617G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP2U1	ENST00000332884.11	c.491-5220G>A		intron_variant		1	NM_183075.3	P1
	ENST00000512428.1	n.1135+371C>T		intron_variant, non_coding_transcript_variant		5
CYP2U1-AS1	ENST00000656249.1	n.81-29201C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.0220

Gnomad4 SAS AF: 0.0680

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.183

Alfa AF: 0.196 Hom.: 4197

Bravo AF: 0.162

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.57

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

Publications

LitVar

Other links and lift over

dbSNP: rs1493131; hg19: chr4-108860906;