rs17537574

chr22-39086622-G-Achr22-39086622-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021822.4(APOBEC3G):c.1024+55G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0673 in 1,530,928 control chromosomes in the GnomAD database, including 3,949 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 0.079 (538 hom., cov: 32)
  • Exomes 𝑓: 0.066 (3411 hom.)
• Consequence: APOBEC3G NM_021822.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOBEC3G	NM_021822.4	c.1024+55G>A		intron_variant		ENST00000407997.4
APOBEC3G	NM_001349436.1	c.991+55G>A		intron_variant
APOBEC3G	NM_001349437.2	c.823+55G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOBEC3G	ENST00000407997.4	c.1024+55G>A		intron_variant		1	NM_021822.4	P1

Frequencies

GnomAD3 genomes AF: 0.0786 AC: 11940 AN: 151998 Hom.: 537 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0877

Gnomad EAS AF: 0.0200

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.0427

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0710

Gnomad OTH AF: 0.0825

GnomAD4 exome AF: 0.0661 AC: 91123 AN: 1378812 Hom.: 3411 AF XY: 0.0643 AC XY: 43537 AN XY: 676970

Gnomad4 AFR exome AF: 0.124

Gnomad4 AMR exome AF: 0.0401

Gnomad4 ASJ exome AF: 0.0823

Gnomad4 EAS exome AF: 0.0240

Gnomad4 SAS exome AF: 0.0160

Gnomad4 FIN exome AF: 0.0448

Gnomad4 NFE exome AF: 0.0709

Gnomad4 OTH exome AF: 0.0656

GnomAD4 genome AF: 0.0786 AC: 11957 AN: 152116 Hom.: 538 Cov.: 32 AF XY: 0.0756 AC XY: 5622 AN XY: 74382

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.0616

Gnomad4 ASJ AF: 0.0877

Gnomad4 EAS AF: 0.0201

Gnomad4 SAS AF: 0.0151

Gnomad4 FIN AF: 0.0427

Gnomad4 NFE AF: 0.0710

Gnomad4 OTH AF: 0.0821

Alfa AF: 0.0458 Hom.: 31

Bravo AF: 0.0829

Asia WGS AF: 0.0300 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.60
Dann	Benign	0.82

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: rs17537574; hg19: chr22-39482627;