Genetic Variant APOBEC3G:c.-144C>G (chr22-39077041-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001349436.1(APOBEC3G):c.-144C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.53 ( 12947 hom., cov: 28)

Exomes 𝑓: 0.65 ( 72107 hom. )

Failed GnomAD Quality Control

Consequence

APOBEC3G
NM_001349436.1 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0400

Publications

6 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

new If you want to explore the variant's impact on the transcript NM_001349436.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.89).

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001349436.1. 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_001349436.1		c.-144C>G	5_prime_UTR	Exon 1 of 8	NP_001336365.1
APOBEC3G	NM_021822.4	MANE Select	c.-321C>G	upstream_gene	N/A	NP_068594.1	Q9HC16-1
APOBEC3G	NM_001349437.2		c.-368C>G	upstream_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.-321C>G	upstream_gene	N/A	ENSP00000385057.3	Q9HC16-1
APOBEC3G	ENST00000960612.1		c.-321C>G	upstream_gene	N/A	ENSP00000630671.1
APOBEC3G	ENST00000851527.1		c.-321C>G	upstream_gene	N/A	ENSP00000521586.1

Frequencies

GnomAD3 genomes

AF:

0.532

AC:

73099

AN:

137346

Hom.:

12946

Cov.:

show subpopulations

Gnomad AFR

AF:

0.547

Gnomad AMI

AF:

0.463

Gnomad AMR

AF:

0.579

Gnomad ASJ

AF:

0.525

Gnomad EAS

AF:

0.600

Gnomad SAS

AF:

0.496

Gnomad FIN

AF:

0.478

Gnomad MID

AF:

0.624

Gnomad NFE

AF:

0.519

Gnomad OTH

AF:

0.557

GnomAD4 exome

AF:

0.654

AC:

219264

AN:

335120

Hom.:

72107

Cov.:

AF XY:

0.650

AC XY:

114338

AN XY:

175920

show subpopulations

African (AFR)

AF:

0.664

AC:

6690

AN:

10070

American (AMR)

AF:

0.741

AC:

10745

AN:

14504

Ashkenazi Jewish (ASJ)

AF:

0.651

AC:

6735

AN:

10352

East Asian (EAS)

AF:

0.752

AC:

16511

AN:

21960

South Asian (SAS)

AF:

0.595

AC:

22285

AN:

37444

European-Finnish (FIN)

AF:

0.555

AC:

10887

AN:

19632

Middle Eastern (MID)

AF:

0.652

AC:

950

AN:

1456

European-Non Finnish (NFE)

AF:

0.657

AC:

131464

AN:

200212

Other (OTH)

AF:

0.667

AC:

12997

AN:

19490

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

3491

6982

10474

13965

17456

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

672

1344

2016

2688

3360

<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

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.532

AC:

73142

AN:

137456

Hom.:

12947

Cov.:

AF XY:

0.525

AC XY:

35215

AN XY:

67064

show subpopulations

African (AFR)

AF:

0.547

AC:

20188

AN:

36906

American (AMR)

AF:

0.579

AC:

7810

AN:

13480

Ashkenazi Jewish (ASJ)

AF:

0.525

AC:

1675

AN:

3190

East Asian (EAS)

AF:

0.599

AC:

2777

AN:

4634

South Asian (SAS)

AF:

0.494

AC:

2188

AN:

4432

European-Finnish (FIN)

AF:

0.478

AC:

4702

AN:

9840

Middle Eastern (MID)

AF:

0.622

AC:

173

AN:

278

European-Non Finnish (NFE)

AF:

0.519

AC:

32159

AN:

61928

Other (OTH)

AF:

0.561

AC:

1081

AN:

1928

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

1446

2892

4339

5785

7231

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

710

1420

2130

2840

3550

<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:

0.424

Hom.:

539

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.5

(source)

DANN

Benign

0.46

PhyloP100

0.040

PromoterAI

-0.43

Neutral

(source)

Mutation Taster

=299/1

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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