Genetic Variant CYP2U1:c.*1706T>C (chr4-107952129-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_183075.3(CYP2U1):c.*1706T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,266 control chromosomes in the GnomAD database, including 2,808 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 0.19 ( 2808 hom., cov: 32)

Exomes 𝑓: 0.33 ( 0 hom. )

Consequence

CYP2U1
NM_183075.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.697

Publications

11 publications found

Variant links:

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 links:

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

CYP2U1-AS1 links:

LOC107986298 (HGNC:):

LOC107986298 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CYP2U1	NM_183075.3 link	c.*1706T>C	3_prime_UTR_variant	Exon 5 of 5	ENST00000332884.11	NP_898898.1	Q7Z449-1
CYP2U1	XM_005262717.2 link	c.*1706T>C	3_prime_UTR_variant	Exon 5 of 5		XP_005262774.1
CYP2U1	XM_005262720.2 link	c.*1706T>C	3_prime_UTR_variant	Exon 4 of 4		XP_005262777.1
LOC107986298	XR_001741784.2 link	n.204+26591A>G	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2U1	ENST00000332884.11 link	c.*1706T>C		3_prime_UTR_variant	Exon 5 of 5	1	NM_183075.3	ENSP00000333212.6		Q7Z449-1

Frequencies

GnomAD3 genomes

AF:

0.186

AC:

28243

AN:

152130

Hom.:

2811

Cov.:

show subpopulations

Gnomad AFR

AF:

0.163

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.162

Gnomad ASJ

AF:

0.233

Gnomad EAS

AF:

0.0225

Gnomad SAS

AF:

0.0721

Gnomad FIN

AF:

0.225

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.217

Gnomad OTH

AF:

0.199

GnomAD4 exome

AF:

0.333

AC:

AN:

Hom.:

Cov.:

AF XY:

0.313

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.417

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.558

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.185

AC:

28231

AN:

152248

Hom.:

2808

Cov.:

AF XY:

0.185

AC XY:

13736

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.162

AC:

6749

AN:

41542

American (AMR)

AF:

0.162

AC:

2479

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.233

AC:

810

AN:

3470

East Asian (EAS)

AF:

0.0225

AC:

117

AN:

5190

South Asian (SAS)

AF:

0.0714

AC:

344

AN:

4820

European-Finnish (FIN)

AF:

0.225

AC:

2389

AN:

10604

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.217

AC:

14754

AN:

68000

Other (OTH)

AF:

0.197

AC:

416

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1169

2337

3506

4674

5843

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.196

Hom.:

5064

Bravo

AF:

0.180

Asia WGS

AF:

0.0580

AC:

200

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

6.8

(source)

DANN

Benign

0.76

PhyloP100

-0.70

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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4-107952129-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over