dbSNP rs35342554: APOBEC3G:c.*406C>T (chr22-39087827-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.*406C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0613 in 232,664 control chromosomes in the GnomAD database, including 2,107 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 0.090 ( 2031 hom., cov: 32)

Exomes 𝑓: 0.0081 ( 76 hom. )

Consequence

APOBEC3G
NM_021822.4 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.07

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:

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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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 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.*406C>T	downstream_gene	N/A	NP_068594.1	Q9HC16-1
APOBEC3G	NM_001349436.1		c.*406C>T	downstream_gene	N/A	NP_001336365.1
APOBEC3G	NM_001349437.2		c.*406C>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.*406C>T	downstream_gene	N/A	ENSP00000385057.3	Q9HC16-1
APOBEC3G	ENST00000960612.1		c.*406C>T	downstream_gene	N/A	ENSP00000630671.1
APOBEC3G	ENST00000851527.1		c.*406C>T	downstream_gene	N/A	ENSP00000521586.1

Frequencies

GnomAD3 genomes

AF:

0.0904

AC:

13560

AN:

150020

Hom.:

2028

Cov.:

show subpopulations

Gnomad AFR

AF:

0.316

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0331

Gnomad ASJ

AF:

0.000292

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00360

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.000773

Gnomad OTH

AF:

0.0658

GnomAD4 exome

AF:

0.00811

AC:

669

AN:

82524

Hom.:

AF XY:

0.00687

AC XY:

313

AN XY:

45558

show subpopulations

African (AFR)

AF:

0.299

AC:

489

AN:

1638

American (AMR)

AF:

0.0186

AC:

AN:

3988

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1838

East Asian (EAS)

AF:

0.00

AC:

AN:

3390

South Asian (SAS)

AF:

0.00213

AC:

AN:

14068

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3026

Middle Eastern (MID)

AF:

0.0127

AC:

AN:

236

European-Non Finnish (NFE)

AF:

0.000692

AC:

AN:

50580

Other (OTH)

AF:

0.0101

AC:

AN:

3760

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

113

141

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:

0.0905

AC:

13585

AN:

150140

Hom.:

2031

Cov.:

AF XY:

0.0876

AC XY:

6429

AN XY:

73376

show subpopulations

African (AFR)

AF:

0.315

AC:

12880

AN:

40838

American (AMR)

AF:

0.0329

AC:

496

AN:

15076

Ashkenazi Jewish (ASJ)

AF:

0.000292

AC:

AN:

3422

East Asian (EAS)

AF:

0.00

AC:

AN:

5056

South Asian (SAS)

AF:

0.00318

AC:

AN:

4716

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10524

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000773

AC:

AN:

67248

Other (OTH)

AF:

0.0660

AC:

136

AN:

2060

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

486

972

1457

1943

2429

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

256

384

512

640

<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:

0.0803

Hom.:

203

Bravo

AF:

0.101

Asia WGS

AF:

0.0280

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.17

(source)

DANN

Benign

0.74

PhyloP100

-2.1

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