rs3093098

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.462
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CYP4F2NM_001082.5 linkc.-1-90T>C intron_variant Intron 1 of 12 ENST00000221700.11 NP_001073.3 P78329-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CYP4F2ENST00000221700.11 linkc.-1-90T>C intron_variant Intron 1 of 12 1 NM_001082.5 ENSP00000221700.3 P78329-1

Frequencies

GnomAD3 genomes
AF:
0.201
AC:
30596
AN:
151940
Hom.:
3512
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.308
Gnomad AMI
AF:
0.0932
Gnomad AMR
AF:
0.176
Gnomad ASJ
AF:
0.215
Gnomad EAS
AF:
0.0838
Gnomad SAS
AF:
0.164
Gnomad FIN
AF:
0.112
Gnomad MID
AF:
0.190
Gnomad NFE
AF:
0.168
Gnomad OTH
AF:
0.216
GnomAD4 exome
AF:
0.160
AC:
214837
AN:
1339144
Hom.:
18457
Cov.:
21
AF XY:
0.160
AC XY:
107150
AN XY:
668078
show subpopulations
Gnomad4 AFR exome
AF:
0.312
AC:
9315
AN:
29900
Gnomad4 AMR exome
AF:
0.109
AC:
3755
AN:
34374
Gnomad4 ASJ exome
AF:
0.206
AC:
4953
AN:
24058
Gnomad4 EAS exome
AF:
0.104
AC:
3925
AN:
37690
Gnomad4 SAS exome
AF:
0.156
AC:
12412
AN:
79356
Gnomad4 FIN exome
AF:
0.107
AC:
4402
AN:
41190
Gnomad4 NFE exome
AF:
0.161
AC:
165898
AN:
1032490
Gnomad4 Remaining exome
AF:
0.167
AC:
9366
AN:
56064
Heterozygous variant carriers
0
6884
13769
20653
27538
34422
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
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:
30639
AN:
152060
Hom.:
3524
Cov.:
31
AF XY:
0.199
AC XY:
14776
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.308
AC:
0.30826
AN:
0.30826
Gnomad4 AMR
AF:
0.176
AC:
0.176082
AN:
0.176082
Gnomad4 ASJ
AF:
0.215
AC:
0.214657
AN:
0.214657
Gnomad4 EAS
AF:
0.0846
AC:
0.0845945
AN:
0.0845945
Gnomad4 SAS
AF:
0.164
AC:
0.164173
AN:
0.164173
Gnomad4 FIN
AF:
0.112
AC:
0.112075
AN:
0.112075
Gnomad4 NFE
AF:
0.168
AC:
0.167996
AN:
0.167996
Gnomad4 OTH
AF:
0.217
AC:
0.216588
AN:
0.216588
Heterozygous variant carriers
0
1168
2337
3505
4674
5842
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
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:
0.170
Hom.:
1675
Bravo
AF:
0.210
Asia WGS
AF:
0.155
AC:
538
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.3
DANN
Benign
0.37
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3093098; hg19: chr19-16008512; API