chr4-107931607-G-A
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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
NM_183075.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.54
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)
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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 | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP2U1 | NM_183075.3 | c.-37G>A | 5_prime_UTR_variant | 1/5 | ENST00000332884.11 | ||
CYP2U1-AS1 | NR_125929.1 | n.149+364C>T | intron_variant, non_coding_transcript_variant | ||||
LOC107986298 | XR_001741784.2 | n.205-21058C>T | intron_variant, non_coding_transcript_variant | ||||
LOC124900751 | XR_007058221.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2U1 | ENST00000332884.11 | c.-37G>A | 5_prime_UTR_variant | 1/5 | 1 | NM_183075.3 | P1 | ||
CYP2U1-AS1 | ENST00000656249.1 | n.81-21058C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0511 AC: 7767AN: 152118Hom.: 432 Cov.: 33
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GnomAD3 exomes AF: 0.0188 AC: 268AN: 14222Hom.: 10 AF XY: 0.0151 AC XY: 123AN XY: 8136
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GnomAD4 exome AF: 0.0191 AC: 20870AN: 1094008Hom.: 425 Cov.: 30 AF XY: 0.0183 AC XY: 9530AN XY: 519634
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GnomAD4 genome AF: 0.0512 AC: 7801AN: 152226Hom.: 438 Cov.: 33 AF XY: 0.0497 AC XY: 3698AN XY: 74426
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
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. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at