dbSNP rs6960775: CYP3A43:c.670+103C>G (chr7-99849797-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_057095.3(CYP3A43):c.670+103C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0881 in 1,154,026 control chromosomes in the GnomAD database, including 10,851 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 0.19 ( 5790 hom., cov: 31)

Exomes 𝑓: 0.072 ( 5061 hom. )

Consequence

CYP3A43
NM_057095.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01

Publications

2 publications found

Variant links:

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]

CYP3A43 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_057095.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CYP3A43	NM_057095.3	MANE Select	c.670+103C>G	intron	N/A	NP_476436.1
CYP3A43	NM_022820.5		c.670+103C>G	intron	N/A	NP_073731.1
CYP3A43	NM_057096.4		c.670+103C>G	intron	N/A	NP_476437.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CYP3A43	ENST00000354829.7	TSL:1 MANE Select	c.670+103C>G	intron	N/A	ENSP00000346887.3
CYP3A43	ENST00000222382.5	TSL:1	c.670+103C>G	intron	N/A	ENSP00000222382.5
CYP3A43	ENST00000312017.9	TSL:1	c.670+103C>G	intron	N/A	ENSP00000312110.5

Frequencies

GnomAD3 genomes

AF:

0.194

AC:

29407

AN:

151708

Hom.:

5769

Cov.:

show subpopulations

Gnomad AFR

AF:

0.509

Gnomad AMI

AF:

0.134

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.0878

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0736

Gnomad FIN

AF:

0.0582

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.0702

Gnomad OTH

AF:

0.170

GnomAD4 exome

AF:

0.0720

AC:

72182

AN:

1002200

Hom.:

5061

Cov.:

AF XY:

0.0715

AC XY:

35644

AN XY:

498864

show subpopulations

African (AFR)

AF:

0.513

AC:

10733

AN:

20914

American (AMR)

AF:

0.0900

AC:

1773

AN:

19708

Ashkenazi Jewish (ASJ)

AF:

0.0882

AC:

1536

AN:

17406

East Asian (EAS)

AF:

0.000415

AC:

AN:

33740

South Asian (SAS)

AF:

0.0682

AC:

3723

AN:

54578

European-Finnish (FIN)

AF:

0.0582

AC:

2035

AN:

34972

Middle Eastern (MID)

AF:

0.105

AC:

317

AN:

3028

European-Non Finnish (NFE)

AF:

0.0622

AC:

48136

AN:

773842

Other (OTH)

AF:

0.0890

AC:

3915

AN:

44012

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

2534

5067

7601

10134

12668

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1756

3512

5268

7024

8780

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.194

AC:

29477

AN:

151826

Hom.:

5790

Cov.:

AF XY:

0.189

AC XY:

14022

AN XY:

74216

show subpopulations

African (AFR)

AF:

0.510

AC:

21025

AN:

41246

American (AMR)

AF:

0.124

AC:

1885

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.0878

AC:

305

AN:

3472

East Asian (EAS)

AF:

0.00135

AC:

AN:

5186

South Asian (SAS)

AF:

0.0737

AC:

355

AN:

4818

European-Finnish (FIN)

AF:

0.0582

AC:

615

AN:

10564

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0702

AC:

4772

AN:

67976

Other (OTH)

AF:

0.169

AC:

356

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

881

1762

2642

3523

4404

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.146

Hom.:

438

Bravo

AF:

0.213

Asia WGS

AF:

0.0600

AC:

211

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.24

(source)

DANN

Benign

0.60

PhyloP100

-1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over