chr22-39086804-G-A

Variant names:

• chr22-39086804-G-A
• rs17537581
• NM_021822.4:c.1025-207G>A

Variant summary

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

The NM_021822.4(APOBEC3G):​c.1025-207G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,044 control chromosomes in the GnomAD database, including 5,822 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 0.21 (5822 hom., cov: 31)
• Consequence: APOBEC3G NM_021822.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 8 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 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.1025-207G>A		intron	N/A	NP_068594.1
	APOBEC3G	NM_001349436.1		c.992-207G>A		intron	N/A	NP_001336365.1
	APOBEC3G	NM_001349437.2		c.824-207G>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.1025-207G>A		intron	N/A	ENSP00000385057.3

Frequencies

GnomAD3 genomes AF: 0.211 AC: 31985 AN: 151926 Hom.: 5818 Cov.: 31

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0274

Gnomad FIN AF: 0.0932

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0998

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.211 AC: 32020 AN: 152044 Hom.: 5822 Cov.: 31 AF XY: 0.204 AC XY: 15158 AN XY: 74328

African (AFR) AF: 0.496 AC: 20545 AN: 41404

American (AMR) AF: 0.135 AC: 2059 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 463 AN: 3470

East Asian (EAS) AF: 0.105 AC: 545 AN: 5166

South Asian (SAS) AF: 0.0263 AC: 127 AN: 4822

European-Finnish (FIN) AF: 0.0932 AC: 989 AN: 10608

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0998 AC: 6784 AN: 67974

Other (OTH) AF: 0.189 AC: 400 AN: 2112

Alfa AF: 0.154 Hom.: 1685

Bravo AF: 0.229

Asia WGS AF: 0.0940 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.44
PhyloP100		-0.043
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: rs17537581; hg19: chr22-39482809;