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GeneBe

rs3093106

chr19-15897447-T-C

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001082.5(CYP4F2):c.165A>G(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 (★).

Frequency

Genomes: 𝑓 0.20 ( 3501 hom., cov: 31)
Exomes 𝑓: 0.17 ( 21428 hom. )

Consequence

CYP4F2
NM_001082.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -5.94
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-5.94 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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
CYP4F2NM_001082.5 linkuse as main transcriptc.165A>G p.Pro55= synonymous_variant 2/13 ENST00000221700.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CYP4F2ENST00000221700.11 linkuse as main transcriptc.165A>G p.Pro55= synonymous_variant 2/131 NM_001082.5 P3P78329-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.201
AC:
30465
AN:
151634
Hom.:
3489
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.307
Gnomad AMI
AF:
0.0932
Gnomad AMR
AF:
0.176
Gnomad ASJ
AF:
0.214
Gnomad EAS
AF:
0.0844
Gnomad SAS
AF:
0.164
Gnomad FIN
AF:
0.112
Gnomad MID
AF:
0.190
Gnomad NFE
AF:
0.168
Gnomad OTH
AF:
0.213
GnomAD3 exomes
AF:
0.162
AC:
40744
AN:
250950
Hom.:
3895
AF XY:
0.163
AC XY:
22165
AN XY:
135654
show subpopulations
Gnomad AFR exome
AF:
0.314
Gnomad AMR exome
AF:
0.114
Gnomad ASJ exome
AF:
0.218
Gnomad EAS exome
AF:
0.0881
Gnomad SAS exome
AF:
0.166
Gnomad FIN exome
AF:
0.115
Gnomad NFE exome
AF:
0.170
Gnomad OTH exome
AF:
0.176
GnomAD4 exome
AF:
0.166
AC:
242703
AN:
1461368
Hom.:
21428
Cov.:
33
AF XY:
0.166
AC XY:
120906
AN XY:
727016
show subpopulations
Gnomad4 AFR exome
AF:
0.323
Gnomad4 AMR exome
AF:
0.121
Gnomad4 ASJ exome
AF:
0.215
Gnomad4 EAS exome
AF:
0.107
Gnomad4 SAS exome
AF:
0.164
Gnomad4 FIN exome
AF:
0.113
Gnomad4 NFE exome
AF:
0.166
Gnomad4 OTH exome
AF:
0.173
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.201
AC:
30508
AN:
151752
Hom.:
3501
Cov.:
31
AF XY:
0.198
AC XY:
14708
AN XY:
74184
show subpopulations
Gnomad4 AFR
AF:
0.308
Gnomad4 AMR
AF:
0.175
Gnomad4 ASJ
AF:
0.214
Gnomad4 EAS
AF:
0.0852
Gnomad4 SAS
AF:
0.164
Gnomad4 FIN
AF:
0.112
Gnomad4 NFE
AF:
0.168
Gnomad4 OTH
AF:
0.214
Alfa
AF:
0.182
Hom.:
3033
Bravo
AF:
0.210
Asia WGS
AF:
0.155
AC:
538
AN:
3478
EpiCase
AF:
0.174
EpiControl
AF:
0.182

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 submitterclinical testingPreventionGenetics, part of Exact SciencesNov 15, 2019This 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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
Cadd
Benign
0.35
Dann
Benign
0.37

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: rs3093106; hg19: chr19-16008257; COSMIC: COSV50000586; COSMIC: COSV50000586; API