19-15897624-A-G
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001082.5(CYP4F2):c.-1-12T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 1,611,402 control chromosomes in the GnomAD database, including 21,117 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 0.15 ( 1832 hom., cov: 31)
Exomes 𝑓: 0.16 ( 19285 hom. )
Consequence
CYP4F2
NM_001082.5 intron
NM_001082.5 intron
Scores
2
Splicing: ADA: 0.00007540
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0600
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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.151 AC: 22877AN: 151884Hom.: 1831 Cov.: 31
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GnomAD3 exomes AF: 0.145 AC: 36149AN: 248510Hom.: 2976 AF XY: 0.150 AC XY: 20171AN XY: 134508
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GnomAD4 exome AF: 0.159 AC: 232369AN: 1459400Hom.: 19285 Cov.: 33 AF XY: 0.160 AC XY: 116134AN XY: 726034
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GnomAD4 genome AF: 0.151 AC: 22895AN: 152002Hom.: 1832 Cov.: 31 AF XY: 0.149 AC XY: 11099AN XY: 74292
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at