NM_021187.4:c.1336G>T

Variant names:

• chr19-15914366-C-A
• NM_021187.4:c.1336G>T

Variant summary

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

The NM_021187.4(CYP4F11):​c.1336G>T​(p.Asp446Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D446N) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 30)
• Consequence: CYP4F11 NM_021187.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.456

Genes affected

CYP4F11 (HGNC:13265): (cytochrome P450 family 4 subfamily F member 11) This gene, CYP4F11, 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 gene is part of a cluster of cytochrome P450 genes on chromosome 19. Another member of this family, CYP4F2, is approximately 16 kb away. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP4F11	NM_021187.4	c.1336G>T	p.Asp446Tyr	missense_variant	Exon 11 of 12	ENST00000402119.9	NP_067010.3
CYP4F11	NM_001128932.2	c.1336G>T	p.Asp446Tyr	missense_variant	Exon 12 of 13		NP_001122404.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP4F11	ENST00000402119.9	c.1336G>T	p.Asp446Tyr	missense_variant	Exon 11 of 12	1	NM_021187.4	ENSP00000384588.2

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 57

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.068	T
BayesDel_noAF	Benign	-0.33
CADD	Benign	11
DANN	Benign	0.24
DEOGEN2	Benign	0.27	T;T;.
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.43	N
LIST_S2	Benign	0.65	.;T;T
M_CAP	Benign	0.0052	T
MetaRNN	Uncertain	0.67	D;D;D
MetaSVM	Benign	-0.91	T
MutationAssessor	Pathogenic	3.1	M;M;.
PrimateAI	Benign	0.47	T
PROVEAN	Pathogenic	-7.7	D;D;.
REVEL	Benign	0.25
Sift	Uncertain	0.012	D;D;.
Sift4G	Uncertain	0.018	D;D;T
Polyphen		0.28	B;B;.
Vest4		0.23
MutPred		0.57		Loss of disorder (P = 0.031);Loss of disorder (P = 0.031);.;
MVP		0.33
MPC		0.042
ClinPred		0.92	D
GERP RS		0.70
Varity_R		0.27
gMVP		0.75

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-16025176;