19-15897702-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001082.5(CYP4F2):c.-1-90T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 1,491,204 control chromosomes in the GnomAD database, including 21,981 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 0.20 ( 3524 hom., cov: 31)
Exomes 𝑓: 0.16 ( 18457 hom. )
Consequence
CYP4F2
NM_001082.5 intron
NM_001082.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.462
Publications
15 publications found
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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.201 AC: 30596AN: 151940Hom.: 3512 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
30596
AN:
151940
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.160 AC: 214837AN: 1339144Hom.: 18457 Cov.: 21 AF XY: 0.160 AC XY: 107150AN XY: 668078 show subpopulations
GnomAD4 exome
AF:
AC:
214837
AN:
1339144
Hom.:
Cov.:
21
AF XY:
AC XY:
107150
AN XY:
668078
show subpopulations
African (AFR)
AF:
AC:
9315
AN:
29900
American (AMR)
AF:
AC:
3755
AN:
34374
Ashkenazi Jewish (ASJ)
AF:
AC:
4953
AN:
24058
East Asian (EAS)
AF:
AC:
3925
AN:
37690
South Asian (SAS)
AF:
AC:
12412
AN:
79356
European-Finnish (FIN)
AF:
AC:
4402
AN:
41190
Middle Eastern (MID)
AF:
AC:
811
AN:
4022
European-Non Finnish (NFE)
AF:
AC:
165898
AN:
1032490
Other (OTH)
AF:
AC:
9366
AN:
56064
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.452
Heterozygous variant carriers
0
6884
13769
20653
27538
34422
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
5814
11628
17442
23256
29070
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.201 AC: 30639AN: 152060Hom.: 3524 Cov.: 31 AF XY: 0.199 AC XY: 14776AN XY: 74358 show subpopulations
GnomAD4 genome
AF:
AC:
30639
AN:
152060
Hom.:
Cov.:
31
AF XY:
AC XY:
14776
AN XY:
74358
show subpopulations
African (AFR)
AF:
AC:
12778
AN:
41452
American (AMR)
AF:
AC:
2693
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
AC:
744
AN:
3466
East Asian (EAS)
AF:
AC:
436
AN:
5154
South Asian (SAS)
AF:
AC:
790
AN:
4812
European-Finnish (FIN)
AF:
AC:
1188
AN:
10600
Middle Eastern (MID)
AF:
AC:
50
AN:
294
European-Non Finnish (NFE)
AF:
AC:
11418
AN:
67966
Other (OTH)
AF:
AC:
457
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.491
Heterozygous variant carriers
0
1168
2337
3505
4674
5842
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
318
636
954
1272
1590
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
538
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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