rs2899313

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOBEC3G	NM_021822.4	c.736-261C>A		intron_variant		ENST00000407997.4
APOBEC3G	NM_001349436.1	c.703-261C>A		intron_variant
APOBEC3G	NM_001349437.2	c.535-261C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOBEC3G	ENST00000407997.4	c.736-261C>A		intron_variant		1	NM_021822.4	P1

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

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.691

Alfa AF: 0.654 Hom.: 51449

Bravo AF: 0.675

Asia WGS AF: 0.702 AC: 2438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.77
DANN	Benign	0.31

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

LitVar

Other links and lift over

dbSNP: rs2899313; hg19: chr22-39482023;