dbSNP rs17537588: 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

Publications

2 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:

Genome browser will be placed here

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

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	UniProt
APOBEC3G	NM_021822.4	MANE Select	c.1141-88G>A	intron	N/A	NP_068594.1	Q9HC16-1
APOBEC3G	NM_001349436.1		c.1108-88G>A	intron	N/A	NP_001336365.1
APOBEC3G	NM_001349437.2		c.940-88G>A	intron	N/A	NP_001336366.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
APOBEC3G	ENST00000407997.4	TSL:1 MANE Select	c.1141-88G>A	intron	N/A	ENSP00000385057.3	Q9HC16-1
APOBEC3G	ENST00000960612.1		c.1138-88G>A	intron	N/A	ENSP00000630671.1
APOBEC3G	ENST00000851527.1		c.577-88G>A	intron	N/A	ENSP00000521586.1

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

Age Distribution

Exome Het

Exome Hom

Variant carriers

426

852

1278

1704

2130

<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:

0.00708

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

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.0103

Hom.:

Bravo

AF:

0.00718

Asia WGS

AF:

0.00231

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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