rs3093199
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001082.5(CYP4F2):c.1398-125A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 1,420,656 control chromosomes in the GnomAD database, including 74,047 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.28 ( 5588 hom., cov: 32)
Exomes 𝑓: 0.34 ( 68459 hom. )
Consequence
CYP4F2
NM_001082.5 intron
NM_001082.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.02
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP4F2 | NM_001082.5 | c.1398-125A>T | intron_variant | ENST00000221700.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP4F2 | ENST00000221700.11 | c.1398-125A>T | intron_variant | 1 | NM_001082.5 | P3 | |||
CYP4F2 | ENST00000011989.11 | c.1398-125A>T | intron_variant | 1 | A1 | ||||
CYP4F2 | ENST00000589654.2 | c.186-125A>T | intron_variant | 3 | |||||
CYP4F2 | ENST00000392846.7 | n.1341-125A>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.279 AC: 41909AN: 150054Hom.: 5577 Cov.: 32
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GnomAD4 exome AF: 0.335 AC: 426181AN: 1270490Hom.: 68459 AF XY: 0.338 AC XY: 210144AN XY: 622440
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GnomAD4 genome ? AF: 0.279 AC: 41947AN: 150166Hom.: 5588 Cov.: 32 AF XY: 0.279 AC XY: 20440AN XY: 73354
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ClinVar
Not reported inComputational scores
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Name
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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