4-107931574-C-T
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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.-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
NM_183075.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.49
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]
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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=-0.78).
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 |
---|---|---|---|---|---|---|---|
CYP2U1 | NM_183075.3 | c.-70C>T | 5_prime_UTR_variant | 1/5 | ENST00000332884.11 | ||
LOC124900751 | XR_007058221.1 | n.12G>A | non_coding_transcript_exon_variant | 1/2 | |||
CYP2U1-AS1 | NR_125929.1 | n.149+397G>A | intron_variant, non_coding_transcript_variant | ||||
LOC107986298 | XR_001741784.2 | n.205-21025G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP2U1 | ENST00000332884.11 | c.-70C>T | 5_prime_UTR_variant | 1/5 | 1 | NM_183075.3 | P1 | ||
CYP2U1-AS1 | ENST00000656249.1 | n.81-21025G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0226 AC: 3445AN: 152192Hom.: 118 Cov.: 33
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GnomAD4 exome AF: 0.00224 AC: 2376AN: 1060226Hom.: 71 Cov.: 25 AF XY: 0.00201 AC XY: 1009AN XY: 501238
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GnomAD4 genome AF: 0.0227 AC: 3457AN: 152304Hom.: 117 Cov.: 33 AF XY: 0.0211 AC XY: 1574AN XY: 74474
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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 submitter | clinical testing | GeneDx | Apr 08, 2019 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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