Variant chr4-107931607-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_183075.3(CYP2U1):c.-37G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.023 in 1,246,234 control chromosomes in the GnomAD database, including 863 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.051 ( 438 hom., cov: 33)

Exomes 𝑓: 0.019 ( 425 hom. )

Consequence

CYP2U1
NM_183075.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.54

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 4-107931607-G-A is Benign according to our data. Variant chr4-107931607-G-A is described in ClinVar as [Benign]. Clinvar id is 380776.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
CYP2U1	NM_183075.3 linkuse as main transcript	c.-37G>A	5_prime_UTR_variant	1/5	ENST00000332884.11
CYP2U1-AS1	NR_125929.1 linkuse as main transcript	n.149+364C>T	intron_variant, non_coding_transcript_variant
LOC107986298	XR_001741784.2 linkuse as main transcript	n.205-21058C>T	intron_variant, non_coding_transcript_variant
LOC124900751	XR_007058221.1 linkuse as main transcript		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP2U1	ENST00000332884.11 linkuse as main transcript	c.-37G>A		5_prime_UTR_variant	1/5	1	NM_183075.3	P1	Q7Z449-1
CYP2U1-AS1	ENST00000656249.1 linkuse as main transcript	n.81-21058C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0511

AC:

7767

AN:

152118

Hom.:

432

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0297

Gnomad ASJ

AF:

0.00893

Gnomad EAS

AF:

0.00637

Gnomad SAS

AF:

0.0182

Gnomad FIN

AF:

0.0178

Gnomad MID

AF:

0.0256

Gnomad NFE

AF:

0.0154

Gnomad OTH

AF:

0.0478

GnomAD3 exomes

AF:

0.0188

AC:

268

AN:

14222

Hom.:

AF XY:

0.0151

AC XY:

123

AN XY:

8136

show subpopulations

Gnomad AFR exome

AF:

0.124

Gnomad AMR exome

AF:

0.0229

Gnomad ASJ exome

AF:

0.00714

Gnomad EAS exome

AF:

0.000627

Gnomad SAS exome

AF:

0.00448

Gnomad FIN exome

AF:

0.00221

Gnomad NFE exome

AF:

0.00959

Gnomad OTH exome

AF:

0.0225

GnomAD4 exome

AF:

0.0191

AC:

20870

AN:

1094008

Hom.:

425

Cov.:

AF XY:

0.0183

AC XY:

9530

AN XY:

519634

show subpopulations

Gnomad4 AFR exome

AF:

0.142

Gnomad4 AMR exome

AF:

0.0269

Gnomad4 ASJ exome

AF:

0.00947

Gnomad4 EAS exome

AF:

0.00719

Gnomad4 SAS exome

AF:

0.0196

Gnomad4 FIN exome

AF:

0.0182

Gnomad4 NFE exome

AF:

0.0160

Gnomad4 OTH exome

AF:

0.0271

GnomAD4 genome

AF:

0.0512

AC:

7801

AN:

152226

Hom.:

438

Cov.:

AF XY:

0.0497

AC XY:

3698

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.141

Gnomad4 AMR

AF:

0.0296

Gnomad4 ASJ

AF:

0.00893

Gnomad4 EAS

AF:

0.00639

Gnomad4 SAS

AF:

0.0182

Gnomad4 FIN

AF:

0.0178

Gnomad4 NFE

AF:

0.0154

Gnomad4 OTH

AF:

0.0473

Alfa

AF:

0.00718

Hom.:

Bravo

AF:

0.0561

Asia WGS

AF:

0.0250

AC:

AN:

3466

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 04, 2016

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.67

DANN

Benign

0.83

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over