19-15889356-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000221700.11(CYP4F2):​c.918+67G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 1,606,332 control chromosomes in the GnomAD database, including 358,341 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 0.64 ( 30822 hom., cov: 31)
Exomes 𝑓: 0.67 ( 327519 hom. )

Consequence

CYP4F2
ENST00000221700.11 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.604
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CYP4F2NM_001082.5 linkuse as main transcriptc.918+67G>A intron_variant ENST00000221700.11 NP_001073.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CYP4F2ENST00000221700.11 linkuse as main transcriptc.918+67G>A intron_variant 1 NM_001082.5 ENSP00000221700 P3P78329-1
CYP4F2ENST00000011989.11 linkuse as main transcriptc.918+67G>A intron_variant 1 ENSP00000011989 A1
CYP4F2ENST00000587671.2 linkuse as main transcriptc.*503+67G>A intron_variant, NMD_transcript_variant 5 ENSP00000467443
CYP4F2ENST00000392846.7 linkuse as main transcriptn.861+67G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.635
AC:
96479
AN:
151826
Hom.:
30809
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.628
Gnomad AMI
AF:
0.534
Gnomad AMR
AF:
0.586
Gnomad ASJ
AF:
0.660
Gnomad EAS
AF:
0.479
Gnomad SAS
AF:
0.702
Gnomad FIN
AF:
0.573
Gnomad MID
AF:
0.649
Gnomad NFE
AF:
0.668
Gnomad OTH
AF:
0.643
GnomAD4 exome
AF:
0.669
AC:
972730
AN:
1454388
Hom.:
327519
AF XY:
0.670
AC XY:
484376
AN XY:
723144
show subpopulations
Gnomad4 AFR exome
AF:
0.637
Gnomad4 AMR exome
AF:
0.527
Gnomad4 ASJ exome
AF:
0.659
Gnomad4 EAS exome
AF:
0.475
Gnomad4 SAS exome
AF:
0.693
Gnomad4 FIN exome
AF:
0.579
Gnomad4 NFE exome
AF:
0.685
Gnomad4 OTH exome
AF:
0.664
GnomAD4 genome
AF:
0.635
AC:
96526
AN:
151944
Hom.:
30822
Cov.:
31
AF XY:
0.629
AC XY:
46716
AN XY:
74270
show subpopulations
Gnomad4 AFR
AF:
0.627
Gnomad4 AMR
AF:
0.585
Gnomad4 ASJ
AF:
0.660
Gnomad4 EAS
AF:
0.480
Gnomad4 SAS
AF:
0.701
Gnomad4 FIN
AF:
0.573
Gnomad4 NFE
AF:
0.668
Gnomad4 OTH
AF:
0.643
Alfa
AF:
0.660
Hom.:
41637
Bravo
AF:
0.631
Asia WGS
AF:
0.596
AC:
2075
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.3
DANN
Benign
0.44

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: rs3093158; hg19: chr19-16000166; COSMIC: COSV50000571; COSMIC: COSV50000571; API