Genetic Variant APOBEC3G:c.1024+55G>A (chr22-39086622-G-A) – 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.1024+55G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0673 in 1,530,928 control chromosomes in the GnomAD database, including 3,949 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 0.079 ( 538 hom., cov: 32)

Exomes 𝑓: 0.066 ( 3411 hom. )

Consequence

APOBEC3G
NM_021822.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0370

Publications

5 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021822.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
APOBEC3G	NM_021822.4	MANE Select	c.1024+55G>A	intron	N/A	NP_068594.1
APOBEC3G	NM_001349436.1		c.991+55G>A	intron	N/A	NP_001336365.1
APOBEC3G	NM_001349437.2		c.823+55G>A	intron	N/A	NP_001336366.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOBEC3G	ENST00000407997.4	TSL:1 MANE Select	c.1024+55G>A		intron	N/A	ENSP00000385057.3

Frequencies

GnomAD3 genomes

AF:

0.0786

AC:

11940

AN:

151998

Hom.:

537

Cov.:

show subpopulations

Gnomad AFR

AF:

0.120

Gnomad AMI

AF:

0.0691

Gnomad AMR

AF:

0.0618

Gnomad ASJ

AF:

0.0877

Gnomad EAS

AF:

0.0200

Gnomad SAS

AF:

0.0153

Gnomad FIN

AF:

0.0427

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0710

Gnomad OTH

AF:

0.0825

GnomAD4 exome

AF:

0.0661

AC:

91123

AN:

1378812

Hom.:

3411

AF XY:

0.0643

AC XY:

43537

AN XY:

676970

show subpopulations

African (AFR)

AF:

0.124

AC:

3807

AN:

30784

American (AMR)

AF:

0.0401

AC:

1363

AN:

33960

Ashkenazi Jewish (ASJ)

AF:

0.0823

AC:

1733

AN:

21046

East Asian (EAS)

AF:

0.0240

AC:

934

AN:

38938

South Asian (SAS)

AF:

0.0160

AC:

1166

AN:

72986

European-Finnish (FIN)

AF:

0.0448

AC:

2240

AN:

50038

Middle Eastern (MID)

AF:

0.0558

AC:

211

AN:

3778

European-Non Finnish (NFE)

AF:

0.0709

AC:

75959

AN:

1070686

Other (OTH)

AF:

0.0656

AC:

3710

AN:

56596

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

4630

9259

13889

18518

23148

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2944

5888

8832

11776

14720

<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:

0.0786

AC:

11957

AN:

152116

Hom.:

538

Cov.:

AF XY:

0.0756

AC XY:

5622

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.121

AC:

4995

AN:

41452

American (AMR)

AF:

0.0616

AC:

942

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0877

AC:

304

AN:

3468

East Asian (EAS)

AF:

0.0201

AC:

104

AN:

5176

South Asian (SAS)

AF:

0.0151

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.0427

AC:

453

AN:

10614

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0710

AC:

4826

AN:

67984

Other (OTH)

AF:

0.0821

AC:

173

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

570

1141

1711

2282

2852

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

130

260

390

520

650

<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:

0.0488

Hom.:

Bravo

AF:

0.0829

Asia WGS

AF:

0.0300

AC:

103

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.60

(source)

DANN

Benign

0.82

PhyloP100

0.037

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