rs17537574

Variant names:

• chr22-39086622-G-A
• rs17537574
• NM_021822.4:c.1024+55G>A

Your query was ambiguous. Multiple possible variants found:

• chr22-39086622-G-A
• chr22-39086622-G-C
• chr22-39086622-G-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.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
• Publications: 5 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOBEC3G	NM_021822.4	MANE Select	c.1024+55G>A		intron	N/A	NP_068594.1	Q9HC16-1
	APOBEC3G	NM_001349436.1		c.991+55G>A		intron	N/A	NP_001336365.1
	APOBEC3G	NM_001349437.2		c.823+55G>A		intron	N/A	NP_001336366.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOBEC3G	ENST00000407997.4	TSL:1 MANE Select	c.1024+55G>A		intron	N/A	ENSP00000385057.3	Q9HC16-1
	APOBEC3G	ENST00000960612.1		c.1021+58G>A		intron	N/A	ENSP00000630671.1
	APOBEC3G	ENST00000851527.1		c.460+55G>A		intron	N/A	ENSP00000521586.1

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

African (AFR) AF: 0.124 AC: 3807 AN: 30784

American (AMR) AF: 0.0401 AC: 1363 AN: 33960

Ashkenazi Jewish (ASJ) AF: 0.0823 AC: 1733 AN: 21046

East Asian (EAS) AF: 0.0240 AC: 934 AN: 38938

South Asian (SAS) AF: 0.0160 AC: 1166 AN: 72986

European-Finnish (FIN) AF: 0.0448 AC: 2240 AN: 50038

Middle Eastern (MID) AF: 0.0558 AC: 211 AN: 3778

European-Non Finnish (NFE) AF: 0.0709 AC: 75959 AN: 1070686

Other (OTH) AF: 0.0656 AC: 3710 AN: 56596

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

African (AFR) AF: 0.121 AC: 4995 AN: 41452

American (AMR) AF: 0.0616 AC: 942 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0877 AC: 304 AN: 3468

East Asian (EAS) AF: 0.0201 AC: 104 AN: 5176

South Asian (SAS) AF: 0.0151 AC: 73 AN: 4820

European-Finnish (FIN) AF: 0.0427 AC: 453 AN: 10614

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0710 AC: 4826 AN: 67984

Other (OTH) AF: 0.0821 AC: 173 AN: 2108

Alfa AF: 0.0488 Hom.: 36

Bravo AF: 0.0829

Asia WGS AF: 0.0300 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.60
DANN	Benign	0.82
PhyloP100		0.037
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: rs17537574; hg19: chr22-39482627;