Genetic Variant APOBEC3G:c.-144C>A (chr22-39077041-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001349436.1(APOBEC3G):c.-144C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000504 in 138,758 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000050 ( 0 hom., cov: 28)

Exomes 𝑓: 0.000074 ( 0 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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOBEC3G	NM_021822.4 link	c.-321C>A		upstream_gene_variant		ENST00000407997.4	NP_068594.1	Q9HC16-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
APOBEC3G	ENST00000407997.4 link	c.-321C>A	upstream_gene_variant	1	NM_021822.4	ENSP00000385057.3	Q9HC16-1
APOBEC3G	ENST00000461827.5 link	n.-43C>A	upstream_gene_variant	3
APOBEC3G	ENST00000463934.1 link	n.-26C>A	upstream_gene_variant	2
APOBEC3G	ENST00000480000.5 link	n.-38C>A	upstream_gene_variant	2

Frequencies

GnomAD3 genomes

AF:

0.0000504

AC:

AN:

138758

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000112

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000744

AC:

AN:

336116

Hom.:

Cov.:

AF XY:

0.0000567

AC XY:

AN XY:

176420

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

10106

American (AMR)

AF:

0.00

AC:

AN:

14534

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

10390

East Asian (EAS)

AF:

0.00

AC:

AN:

22028

South Asian (SAS)

AF:

0.00

AC:

AN:

37516

European-Finnish (FIN)

AF:

0.00

AC:

AN:

19708

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1466

European-Non Finnish (NFE)

AF:

0.000115

AC:

AN:

200824

Other (OTH)

AF:

0.000102

AC:

AN:

19544

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0000504

AC:

AN:

138758

Hom.:

Cov.:

AF XY:

0.0000443

AC XY:

AN XY:

67738

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

37210

American (AMR)

AF:

0.00

AC:

AN:

13592

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3224

East Asian (EAS)

AF:

0.00

AC:

AN:

4682

South Asian (SAS)

AF:

0.00

AC:

AN:

4494

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9918

Middle Eastern (MID)

AF:

0.00

AC:

AN:

298

European-Non Finnish (NFE)

AF:

0.000112

AC:

AN:

62572

Other (OTH)

AF:

0.00

AC:

AN:

1922

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.446

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

539

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.9

(source)

DANN

Benign

0.61

PhyloP100

0.040

PromoterAI

-0.55

Under-expression

(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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over