chr19-15889799-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001082.5(CYP4F2):​c.648-106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

CYP4F2
NM_001082.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.311

Publications

9 publications found
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: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CYP4F2NM_001082.5 linkc.648-106A>G intron_variant Intron 6 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.648-106A>G intron_variant Intron 6 of 12 1 NM_001082.5 ENSP00000221700.3 P78329-1
CYP4F2ENST00000011989.11 linkc.648-106A>G intron_variant Intron 6 of 12 1 ENSP00000011989.8 A0A0A0MQR0
CYP4F2ENST00000392846.7 linkn.591-106A>G intron_variant Intron 4 of 10 2
CYP4F2ENST00000587671.2 linkn.*233-106A>G intron_variant Intron 5 of 7 5 ENSP00000467443.2 K7EPM0

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1352104
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
668330
African (AFR)
AF:
0.00
AC:
0
AN:
30670
American (AMR)
AF:
0.00
AC:
0
AN:
37472
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
21278
East Asian (EAS)
AF:
0.00
AC:
0
AN:
38914
South Asian (SAS)
AF:
0.00
AC:
0
AN:
74388
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
50038
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5190
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1038156
Other (OTH)
AF:
0.00
AC:
0
AN:
55998
GnomAD4 genome
Cov.:
31
Alfa
AF:
0.00
Hom.:
1205

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
3.1
DANN
Benign
0.49
PhyloP100
-0.31

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs3093156; hg19: chr19-16000609; API