rs472660

Positions:

• chr7-99862484-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_057095.3(CYP3A43):​c.1253+645G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,076 control chromosomes in the GnomAD database, including 9,635 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 0.27 (9635 hom., cov: 32)
• Consequence: CYP3A43 NM_057095.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

Genes affected

CYP3A43 (HGNC:17450): (cytochrome P450 family 3 subfamily A member 43) 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. The encoded protein has a low level of testosterone hydroxylase activity, and may play a role in aging mechanisms and cancer progression. This gene is part of a cluster of cytochrome P450 genes on chromosome 7q21.1. Alternate splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP3A43	NM_057095.3	c.1253+645G>A		intron_variant		ENST00000354829.7	NP_476436.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP3A43	ENST00000354829.7	c.1253+645G>A		intron_variant		1	NM_057095.3	ENSP00000346887	A1

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40719 AN: 151958 Hom.: 9604 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.244

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.268 AC: 40801 AN: 152076 Hom.: 9635 Cov.: 32 AF XY: 0.262 AC XY: 19507 AN XY: 74392

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.243

Alfa AF: 0.153 Hom.: 1907

Bravo AF: 0.288

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.43

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

Other links and lift over

dbSNP: rs472660; hg19: chr7-99460107;