7-99768384-C-A

Variant names:

• chr7-99768384-C-A
• NM_017460.6:c.640G>T

Variant summary

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

The NM_017460.6(CYP3A4):​c.640G>T​(p.Asp214Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CYP3A4 NM_017460.6 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -2.12

Genes affected

CYP3A4 (HGNC:2637): (cytochrome P450 family 3 subfamily A member 4) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases that catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum and its expression is induced by glucocorticoids and some pharmacological agents. This enzyme is involved in the metabolism of approximately half the drugs in use today, including acetaminophen, codeine, cyclosporin A, diazepam, erythromycin, and chloroquine. The enzyme also metabolizes some steroids and carcinogens. This gene is part of a cluster of cytochrome P450 genes on chromosome 7q21.1. Previously another CYP3A gene, CYP3A3, was thought to exist; however, it is now thought that this sequence represents a transcript variant of CYP3A4. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Aug 2020]

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
CYP3A4	NM_017460.6	c.640G>T	p.Asp214Tyr	missense_variant	Exon 7 of 13	ENST00000651514.1	NP_059488.2
CYP3A4	NM_001202855.3	c.640G>T	p.Asp214Tyr	missense_variant	Exon 7 of 13		NP_001189784.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP3A4	ENST00000651514.1	c.640G>T	p.Asp214Tyr	missense_variant	Exon 7 of 13		NM_017460.6	ENSP00000498939.1
CYP3A4	ENST00000336411.7	c.640G>T	p.Asp214Tyr	missense_variant	Exon 7 of 14	1		ENSP00000337915.3
CYP3A4	ENST00000652018.1	c.493G>T	p.Asp165Tyr	missense_variant	Exon 5 of 11			ENSP00000498733.1
CYP3A4	ENST00000354593.6	c.190G>T	p.Asp64Tyr	missense_variant	Exon 2 of 8	5		ENSP00000346607.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

May 14, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.640G>T (p.D214Y) alteration is located in exon 7 (coding exon 7) of the CYP3A4 gene. This alteration results from a G to T substitution at nucleotide position 640, causing the aspartic acid (D) at amino acid position 214 to be replaced by a tyrosine (Y). 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	0.24
BayesDel_addAF	Benign	-0.076	T
BayesDel_noAF	Benign	-0.35
CADD	Benign	13
DANN	Benign	0.95
DEOGEN2	Benign	0.080	T;T
Eigen	Benign	-0.93
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.051	N
LIST_S2	Benign	0.70	T;T
M_CAP	Benign	0.049	D
MetaRNN	Uncertain	0.63	D;D
MetaSVM	Benign	-0.62	T
MutationAssessor	Pathogenic	2.9	.;M
PrimateAI	Benign	0.28	T
PROVEAN	Uncertain	-4.3	D;D
REVEL	Benign	0.29
Sift	Uncertain	0.0040	D;D
Sift4G	Uncertain	0.0090	D;D
Polyphen		0.95	P;P
Vest4		0.40
MutPred		0.72		.;Loss of stability (P = 0.0765);
MVP		0.55
MPC		0.36
ClinPred		0.64	D
GERP RS		-8.6
Varity_R		0.29

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: chr7-99366007;