rs2899313

Variant names:

• chr22-39086018-C-A
• rs2899313
• NM_021822.4:c.736-261C>A

Your query was ambiguous. Multiple possible variants found:

• chr22-39086018-C-A
• chr22-39086018-C-T

Variant summary

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

The NM_021822.4(APOBEC3G):​c.736-261C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,722 control chromosomes in the GnomAD database, including 32,897 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 0.66 (32897 hom., cov: 31)
• Consequence: APOBEC3G NM_021822.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.941
• Publications: 10 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOBEC3G	NM_021822.4	MANE Select	c.736-261C>A		intron	N/A	NP_068594.1
	APOBEC3G	NM_001349436.1		c.703-261C>A		intron	N/A	NP_001336365.1
	APOBEC3G	NM_001349437.2		c.535-261C>A		intron	N/A	NP_001336366.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOBEC3G	ENST00000407997.4	TSL:1 MANE Select	c.736-261C>A		intron	N/A	ENSP00000385057.3
	APOBEC3G	ENST00000960612.1		c.736-261C>A		intron	N/A	ENSP00000630671.1
	APOBEC3G	ENST00000851527.1		c.172-261C>A		intron	N/A	ENSP00000521586.1

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99667 AN: 151606 Hom.: 32883 Cov.: 31

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.657 AC: 99723 AN: 151722 Hom.: 32897 Cov.: 31 AF XY: 0.652 AC XY: 48329 AN XY: 74128

African (AFR) AF: 0.673 AC: 27832 AN: 41346

American (AMR) AF: 0.724 AC: 11036 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2285 AN: 3470

East Asian (EAS) AF: 0.754 AC: 3880 AN: 5146

South Asian (SAS) AF: 0.576 AC: 2766 AN: 4802

European-Finnish (FIN) AF: 0.547 AC: 5757 AN: 10526

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.648 AC: 43970 AN: 67874

Other (OTH) AF: 0.691 AC: 1458 AN: 2110

Alfa AF: 0.656 Hom.: 83198

Bravo AF: 0.675

Asia WGS AF: 0.702 AC: 2438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.77
DANN	Benign	0.31
PhyloP100		-0.94
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: rs2899313; hg19: chr22-39482023;