Genetic Variant APOBEC3G:c.1141-88G>A (chr22-39087319-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_021822.4(APOBEC3G):c.1141-88G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00911 in 1,604,596 control chromosomes in the GnomAD database, including 76 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 0.0071 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0093 ( 73 hom. )

Consequence

APOBEC3G
NM_021822.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.69

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 -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.05).

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
APOBEC3G	NM_021822.4 link	c.1141-88G>A	intron_variant	Intron 7 of 7	ENST00000407997.4	NP_068594.1	Q9HC16-1
APOBEC3G	NM_001349436.1 link	c.1108-88G>A	intron_variant	Intron 7 of 7		NP_001336365.1
APOBEC3G	NM_001349437.2 link	c.940-88G>A	intron_variant	Intron 6 of 6		NP_001336366.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOBEC3G	ENST00000407997.4 link	c.1141-88G>A		intron_variant	Intron 7 of 7	1	NM_021822.4	ENSP00000385057.3		Q9HC16-1

Frequencies

GnomAD3 genomes

AF:

0.00709

AC:

1076

AN:

151796

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00184

Gnomad AMI

AF:

0.0286

Gnomad AMR

AF:

0.00689

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00501

Gnomad FIN

AF:

0.00397

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0107

Gnomad OTH

AF:

0.00958

GnomAD4 exome

AF:

0.00932

AC:

13540

AN:

1452682

Hom.:

Cov.:

AF XY:

0.00930

AC XY:

6724

AN XY:

723386

show subpopulations

African (AFR)

AF:

0.00150

AC:

AN:

33252

American (AMR)

AF:

0.00680

AC:

304

AN:

44714

Ashkenazi Jewish (ASJ)

AF:

0.0148

AC:

387

AN:

26076

East Asian (EAS)

AF:

0.00

AC:

AN:

39642

South Asian (SAS)

AF:

0.00440

AC:

379

AN:

86052

European-Finnish (FIN)

AF:

0.00406

AC:

217

AN:

53408

Middle Eastern (MID)

AF:

0.0157

AC:

AN:

5750

European-Non Finnish (NFE)

AF:

0.0105

AC:

11555

AN:

1103720

Other (OTH)

AF:

0.00929

AC:

558

AN:

60068

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

765

1530

2296

3061

3826

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00708

AC:

1076

AN:

151914

Hom.:

Cov.:

AF XY:

0.00668

AC XY:

496

AN XY:

74246

show subpopulations

African (AFR)

AF:

0.00184

AC:

AN:

41410

American (AMR)

AF:

0.00689

AC:

105

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.0150

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5166

South Asian (SAS)

AF:

0.00502

AC:

AN:

4784

European-Finnish (FIN)

AF:

0.00397

AC:

AN:

10576

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0107

AC:

727

AN:

67942

Other (OTH)

AF:

0.00948

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

148

198

247

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0103

Hom.:

Bravo

AF:

0.00718

Asia WGS

AF:

0.00231

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.75

(source)

DANN

Benign

0.57

PhyloP100

-4.7

Mutation Taster

=100/0

polymorphism

(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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chr22-39087319-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over