chr19-15878848-T-C

Variant names:

• chr19-15878848-T-C
• NM_001082.5:c.1486A>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001082.5(CYP4F2):​c.1486A>G​(p.Thr496Ala) variant causes a missense 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. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: CYP4F2 NM_001082.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.332

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.0750522).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP4F2	NM_001082.5	c.1486A>G	p.Thr496Ala	missense_variant	Exon 13 of 13	ENST00000221700.11	NP_001073.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP4F2	ENST00000221700.11	c.1486A>G	p.Thr496Ala	missense_variant	Exon 13 of 13	1	NM_001082.5	ENSP00000221700.3
CYP4F2	ENST00000011989.11	c.1486A>G	p.Thr496Ala	missense_variant	Exon 13 of 13	1		ENSP00000011989.8
CYP4F2	ENST00000589654.2	c.*51A>G		3_prime_UTR_variant	Exon 3 of 3	3		ENSP00000467846.1
CYP4F2	ENST00000392846.7	n.1429A>G		non_coding_transcript_exon_variant	Exon 11 of 11	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Feb 13, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1486A>G (p.T496A) alteration is located in exon 13 (coding exon 12) of the CYP4F2 gene. This alteration results from a A to G substitution at nucleotide position 1486, causing the threonine (T) at amino acid position 496 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.059
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.60
CADD	Benign	3.0
DANN	Benign	0.67
DEOGEN2	Benign	0.040	T;.
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.012	N
LIST_S2	Benign	0.0077	T;T
M_CAP	Benign	0.0054	T
MetaRNN	Benign	0.075	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.53	N;.
PrimateAI	Benign	0.47	T
PROVEAN	Benign	-1.8	N;.
REVEL	Benign	0.043
Sift	Benign	0.41	T;.
Sift4G	Benign	0.43	T;T
Polyphen		0.0	B;.
Vest4		0.063
MutPred		0.24		Loss of phosphorylation at T496 (P = 0.026);Loss of phosphorylation at T496 (P = 0.026);
MVP		0.44
MPC		0.15
ClinPred		0.021	T
GERP RS		-1.3
Varity_R		0.060
gMVP		0.63

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-15989658;