Genetic Variant APOBEC3G:c.467-85T>C (chr22-39081386-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_021822.4(APOBEC3G):c.467-85T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0491 in 1,531,826 control chromosomes in the GnomAD database, including 6,158 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 0.13 ( 2992 hom., cov: 32)

Exomes 𝑓: 0.040 ( 3166 hom. )

Consequence

APOBEC3G
NM_021822.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19

Publications

8 publications found

Variant links:

Genes affected

APOBEC3G (HGNC:17357): (apolipoprotein B mRNA editing enzyme catalytic subunit 3G) This gene is a member of the cytidine deaminase gene family. It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22. Members of the cluster encode proteins that are structurally and functionally related to the C to U RNA-editing cytidine deaminase APOBEC1. The protein encoded by this gene catalyzes site-specific deamination of both RNA and single-stranded DNA. The encoded protein has been found to be a specific inhibitor of human immunodeficiency virus-1 (HIV-1) infectivity. [provided by RefSeq, Mar 2017]

APOBEC3G 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOBEC3G	NM_021822.4 link	c.467-85T>C		intron_variant	Intron 3 of 7	ENST00000407997.4	NP_068594.1	Q9HC16-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOBEC3G	ENST00000407997.4 link	c.467-85T>C		intron_variant	Intron 3 of 7	1	NM_021822.4	ENSP00000385057.3		Q9HC16-1

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19738

AN:

152030

Hom.:

2990

Cov.:

show subpopulations

Gnomad AFR

AF:

0.368

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0719

Gnomad ASJ

AF:

0.0455

Gnomad EAS

AF:

0.0856

Gnomad SAS

AF:

0.0132

Gnomad FIN

AF:

0.0516

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0287

Gnomad OTH

AF:

0.106

GnomAD4 exome

AF:

0.0401

AC:

55380

AN:

1379678

Hom.:

3166

Cov.:

AF XY:

0.0381

AC XY:

26238

AN XY:

688462

show subpopulations

African (AFR)

AF:

0.376

AC:

11833

AN:

31456

American (AMR)

AF:

0.0617

AC:

2601

AN:

42144

Ashkenazi Jewish (ASJ)

AF:

0.0477

AC:

1134

AN:

23758

East Asian (EAS)

AF:

0.0775

AC:

3051

AN:

39346

South Asian (SAS)

AF:

0.0129

AC:

1045

AN:

80752

European-Finnish (FIN)

AF:

0.0481

AC:

2395

AN:

49816

Middle Eastern (MID)

AF:

0.0502

AC:

272

AN:

5414

European-Non Finnish (NFE)

AF:

0.0284

AC:

29835

AN:

1049700

Other (OTH)

AF:

0.0561

AC:

3214

AN:

57292

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

2552

5103

7655

10206

12758

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1314

2628

3942

5256

6570

<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:

0.130

AC:

19757

AN:

152148

Hom.:

2992

Cov.:

AF XY:

0.126

AC XY:

9395

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.368

AC:

15254

AN:

41456

American (AMR)

AF:

0.0717

AC:

1096

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0455

AC:

158

AN:

3472

East Asian (EAS)

AF:

0.0858

AC:

444

AN:

5172

South Asian (SAS)

AF:

0.0126

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.0516

AC:

548

AN:

10612

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0288

AC:

1956

AN:

67996

Other (OTH)

AF:

0.104

AC:

220

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

708

1416

2125

2833

3541

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<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:

0.0604

Hom.:

3600

Bravo

AF:

0.143

Asia WGS

AF:

0.0660

AC:

230

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.59

(source)

DANN

Benign

0.49

PhyloP100

-1.2

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over