4-107931574-C-T

Variant summary

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

The NM_183075.3(CYP2U1):​c.-70C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00481 in 1,212,530 control chromosomes in the GnomAD database, including 188 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.023 ( 117 hom., cov: 33)
Exomes 𝑓: 0.0022 ( 71 hom. )

Consequence

CYP2U1
NM_183075.3 5_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.49
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-AS1 (HGNC:54817): (CYP2U1 and SGMS2 antisense RNA 1)

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=-0.78).
BP6
Variant 4-107931574-C-T is Benign according to our data. Variant chr4-107931574-C-T is described in ClinVar as [Benign]. Clinvar id is 1242157.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0751 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CYP2U1NM_183075.3 linkuse as main transcriptc.-70C>T 5_prime_UTR_variant 1/5 ENST00000332884.11
LOC124900751XR_007058221.1 linkuse as main transcriptn.12G>A non_coding_transcript_exon_variant 1/2
CYP2U1-AS1NR_125929.1 linkuse as main transcriptn.149+397G>A intron_variant, non_coding_transcript_variant
LOC107986298XR_001741784.2 linkuse as main transcriptn.205-21025G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CYP2U1ENST00000332884.11 linkuse as main transcriptc.-70C>T 5_prime_UTR_variant 1/51 NM_183075.3 P1Q7Z449-1
CYP2U1-AS1ENST00000656249.1 linkuse as main transcriptn.81-21025G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0226
AC:
3445
AN:
152192
Hom.:
118
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0772
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00988
Gnomad ASJ
AF:
0.00231
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000413
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00955
Gnomad NFE
AF:
0.000647
Gnomad OTH
AF:
0.0177
GnomAD4 exome
AF:
0.00224
AC:
2376
AN:
1060226
Hom.:
71
Cov.:
25
AF XY:
0.00201
AC XY:
1009
AN XY:
501238
show subpopulations
Gnomad4 AFR exome
AF:
0.0755
Gnomad4 AMR exome
AF:
0.00936
Gnomad4 ASJ exome
AF:
0.00197
Gnomad4 EAS exome
AF:
0.0000400
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000473
Gnomad4 NFE exome
AF:
0.000306
Gnomad4 OTH exome
AF:
0.00712
GnomAD4 genome
AF:
0.0227
AC:
3457
AN:
152304
Hom.:
117
Cov.:
33
AF XY:
0.0211
AC XY:
1574
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.0773
Gnomad4 AMR
AF:
0.00986
Gnomad4 ASJ
AF:
0.00231
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000632
Gnomad4 OTH
AF:
0.0175
Alfa
AF:
0.000860
Hom.:
2
Bravo
AF:
0.0263
Asia WGS
AF:
0.00376
AC:
13
AN:
3474

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxApr 08, 2019- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
3.2
DANN
Benign
0.88

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.

Other links and lift over

dbSNP: rs139667669; hg19: chr4-108852730; API