19-15885914-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001082.5(CYP4F2):​c.1115+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00516 in 1,612,376 control chromosomes in the GnomAD database, including 276 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.022 ( 120 hom., cov: 31)
Exomes 𝑓: 0.0034 ( 156 hom. )

Consequence

CYP4F2
NM_001082.5 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.247
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 made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 19-15885914-C-T is Benign according to our data. Variant chr19-15885914-C-T is described in ClinVar as [Benign]. Clinvar id is 771214.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0714 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CYP4F2NM_001082.5 linkuse as main transcriptc.1115+10G>A intron_variant ENST00000221700.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CYP4F2ENST00000221700.11 linkuse as main transcriptc.1115+10G>A intron_variant 1 NM_001082.5 P3P78329-1

Frequencies

GnomAD3 genomes
AF:
0.0219
AC:
3334
AN:
152144
Hom.:
120
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0735
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00733
Gnomad ASJ
AF:
0.0130
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00663
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.000985
Gnomad OTH
AF:
0.0148
GnomAD3 exomes
AF:
0.00774
AC:
1936
AN:
249996
Hom.:
59
AF XY:
0.00643
AC XY:
868
AN XY:
135064
show subpopulations
Gnomad AFR exome
AF:
0.0762
Gnomad AMR exome
AF:
0.00711
Gnomad ASJ exome
AF:
0.0140
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00572
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000771
Gnomad OTH exome
AF:
0.00837
GnomAD4 exome
AF:
0.00341
AC:
4973
AN:
1460114
Hom.:
156
Cov.:
30
AF XY:
0.00331
AC XY:
2405
AN XY:
726354
show subpopulations
Gnomad4 AFR exome
AF:
0.0805
Gnomad4 AMR exome
AF:
0.00746
Gnomad4 ASJ exome
AF:
0.0120
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00623
Gnomad4 FIN exome
AF:
0.0000188
Gnomad4 NFE exome
AF:
0.000488
Gnomad4 OTH exome
AF:
0.00811
GnomAD4 genome
AF:
0.0220
AC:
3348
AN:
152262
Hom.:
120
Cov.:
31
AF XY:
0.0216
AC XY:
1609
AN XY:
74480
show subpopulations
Gnomad4 AFR
AF:
0.0736
Gnomad4 AMR
AF:
0.00732
Gnomad4 ASJ
AF:
0.0130
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00622
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000985
Gnomad4 OTH
AF:
0.0147
Alfa
AF:
0.00911
Hom.:
40
Bravo
AF:
0.0249
Asia WGS
AF:
0.00779
AC:
27
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJul 23, 2018- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
CYP4F2-related disorder Benign:1
Benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesJul 12, 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
-0.82
CADD
Benign
6.8
DANN
Benign
0.80

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: rs3093161; hg19: chr19-15996724; API