22-39083569-C-G

Variant names:

• chr22-39083569-C-G
• rs2294367
• NM_021822.4:c.582-162C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021822.4(APOBEC3G):​c.582-162C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,640 control chromosomes in the GnomAD database, including 17,391 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 0.44 (17391 hom., cov: 30)
• Consequence: APOBEC3G NM_021822.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 9 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOBEC3G	NM_021822.4	c.582-162C>G		intron_variant	Intron 4 of 7	ENST00000407997.4	NP_068594.1
APOBEC3G	NM_001349436.1	c.549-162C>G		intron_variant	Intron 4 of 7		NP_001336365.1
APOBEC3G	NM_001349437.2	c.381-162C>G		intron_variant	Intron 3 of 6		NP_001336366.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOBEC3G	ENST00000407997.4	c.582-162C>G		intron_variant	Intron 4 of 7	1	NM_021822.4	ENSP00000385057.3
APOBEC3G	ENST00000461827.5	n.650-162C>G		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67391 AN: 151522 Hom.: 17385 Cov.: 30

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.496

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.445 AC: 67404 AN: 151640 Hom.: 17391 Cov.: 30 AF XY: 0.447 AC XY: 33065 AN XY: 74046

African (AFR) AF: 0.165 AC: 6806 AN: 41336

American (AMR) AF: 0.586 AC: 8944 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1826 AN: 3460

East Asian (EAS) AF: 0.648 AC: 3292 AN: 5082

South Asian (SAS) AF: 0.574 AC: 2759 AN: 4806

European-Finnish (FIN) AF: 0.461 AC: 4848 AN: 10514

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.549 AC: 37244 AN: 67882

Other (OTH) AF: 0.501 AC: 1055 AN: 2106

Alfa AF: 0.341 Hom.: 1012

Bravo AF: 0.443

Asia WGS AF: 0.612 AC: 2126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.89
DANN	Benign	0.37
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2294367; hg19: chr22-39479574;