rs3093106
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001082.5(CYP4F2):āc.165A>Gā(p.Pro55=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 1,613,120 control chromosomes in the GnomAD database, including 24,929 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.20 ( 3501 hom., cov: 31)
Exomes š: 0.17 ( 21428 hom. )
Consequence
CYP4F2
NM_001082.5 synonymous
NM_001082.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.94
Genes affected
CYP4F2 (HGNC:2645): (cytochrome P450 family 4 subfamily F member 2) 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 protein localizes to the endoplasmic reticulum. The enzyme starts the process of inactivating and degrading leukotriene B4, a potent mediator of inflammation. This gene is part of a cluster of cytochrome P450 genes on chromosome 19. Another member of this family, CYP4F11, is approximately 16 kb away. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BP6
?
Variant 19-15897447-T-C is Benign according to our data. Variant chr19-15897447-T-C is described in ClinVar as [Benign]. Clinvar id is 3060298.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-5.94 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP4F2 | NM_001082.5 | c.165A>G | p.Pro55= | synonymous_variant | 2/13 | ENST00000221700.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP4F2 | ENST00000221700.11 | c.165A>G | p.Pro55= | synonymous_variant | 2/13 | 1 | NM_001082.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.201 AC: 30465AN: 151634Hom.: 3489 Cov.: 31
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GnomAD3 exomes AF: 0.162 AC: 40744AN: 250950Hom.: 3895 AF XY: 0.163 AC XY: 22165AN XY: 135654
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GnomAD4 exome AF: 0.166 AC: 242703AN: 1461368Hom.: 21428 Cov.: 33 AF XY: 0.166 AC XY: 120906AN XY: 727016
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GnomAD4 genome ? AF: 0.201 AC: 30508AN: 151752Hom.: 3501 Cov.: 31 AF XY: 0.198 AC XY: 14708AN XY: 74184
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CYP4F2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 15, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at