rs17537588

Positions:

• chr22-39087319-G-A
• chr22-39087319-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_021822.4(APOBEC3G):​c.1141-88G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00911 in 1,604,596 control chromosomes in the GnomAD database, including 76 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 0.0071 (3 hom., cov: 32)
  • Exomes 𝑓: 0.0093 (73 hom.)
• Consequence: APOBEC3G NM_021822.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.69

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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOBEC3G	NM_021822.4	c.1141-88G>A		intron_variant		ENST00000407997.4	NP_068594.1
APOBEC3G	NM_001349436.1	c.1108-88G>A		intron_variant			NP_001336365.1
APOBEC3G	NM_001349437.2	c.940-88G>A		intron_variant			NP_001336366.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOBEC3G	ENST00000407997.4	c.1141-88G>A		intron_variant		1	NM_021822.4	ENSP00000385057	P1

Frequencies

GnomAD3 genomes AF: 0.00709 AC: 1076 AN: 151796 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.00184

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.00689

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00501

Gnomad FIN AF: 0.00397

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0107

Gnomad OTH AF: 0.00958

GnomAD4 exome AF: 0.00932 AC: 13540 AN: 1452682 Hom.: 73 Cov.: 31 AF XY: 0.00930 AC XY: 6724 AN XY: 723386

Gnomad4 AFR exome AF: 0.00150

Gnomad4 AMR exome AF: 0.00680

Gnomad4 ASJ exome AF: 0.0148

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00440

Gnomad4 FIN exome AF: 0.00406

Gnomad4 NFE exome AF: 0.0105

Gnomad4 OTH exome AF: 0.00929

GnomAD4 genome AF: 0.00708 AC: 1076 AN: 151914 Hom.: 3 Cov.: 32 AF XY: 0.00668 AC XY: 496 AN XY: 74246

Gnomad4 AFR AF: 0.00184

Gnomad4 AMR AF: 0.00689

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00502

Gnomad4 FIN AF: 0.00397

Gnomad4 NFE AF: 0.0107

Gnomad4 OTH AF: 0.00948

Alfa AF: 0.0103 Hom.: 1

Bravo AF: 0.00718

Asia WGS AF: 0.00231 AC: 8 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.75
DANN	Benign	0.57

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: rs17537588; hg19: chr22-39483324;