Genetic Variant APOBEC3G:c.*418C>T (chr22-39087839-C-T) – 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.*418C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0553 in 227,608 control chromosomes in the GnomAD database, including 1,679 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 0.080 ( 1628 hom., cov: 32)

Exomes 𝑓: 0.0064 ( 51 hom. )

Consequence

APOBEC3G
NM_021822.4 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.27

Publications

11 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 = 0.273 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	UniProt
APOBEC3G	NM_021822.4	MANE Select	c.*418C>T	downstream_gene	N/A	NP_068594.1	Q9HC16-1
APOBEC3G	NM_001349436.1		c.*418C>T	downstream_gene	N/A	NP_001336365.1
APOBEC3G	NM_001349437.2		c.*418C>T	downstream_gene	N/A	NP_001336366.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
APOBEC3G	ENST00000407997.4	TSL:1 MANE Select	c.*418C>T	downstream_gene	N/A	ENSP00000385057.3	Q9HC16-1
APOBEC3G	ENST00000960612.1		c.*418C>T	downstream_gene	N/A	ENSP00000630671.1
APOBEC3G	ENST00000851527.1		c.*418C>T	downstream_gene	N/A	ENSP00000521586.1

Frequencies

GnomAD3 genomes

AF:

0.0795

AC:

12079

AN:

151948

Hom.:

1627

Cov.:

show subpopulations

Gnomad AFR

AF:

0.278

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0284

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.000706

Gnomad OTH

AF:

0.0566

GnomAD4 exome

AF:

0.00635

AC:

480

AN:

75542

Hom.:

AF XY:

0.00526

AC XY:

219

AN XY:

41674

show subpopulations

African (AFR)

AF:

0.261

AC:

357

AN:

1368

American (AMR)

AF:

0.0155

AC:

AN:

3812

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1600

East Asian (EAS)

AF:

0.00

AC:

AN:

3106

South Asian (SAS)

AF:

0.000534

AC:

AN:

13098

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2792

Middle Eastern (MID)

AF:

0.0100

AC:

AN:

200

European-Non Finnish (NFE)

AF:

0.000629

AC:

AN:

46088

Other (OTH)

AF:

0.00748

AC:

AN:

3478

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome 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

GnomAD4 genome

AF:

0.0796

AC:

12097

AN:

152066

Hom.:

1628

Cov.:

AF XY:

0.0770

AC XY:

5728

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.278

AC:

11488

AN:

41384

American (AMR)

AF:

0.0283

AC:

432

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.000288

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5192

South Asian (SAS)

AF:

0.00104

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10604

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000706

AC:

AN:

68002

Other (OTH)

AF:

0.0560

AC:

118

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

439

878

1318

1757

2196

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<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:

0.0151

Hom.:

Bravo

AF:

0.0896

Asia WGS

AF:

0.0170

AC:

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

0.21

(source)

DANN

Benign

0.68

PhyloP100

-2.3

Splicing

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