chr22-39080377-A-G

Variant names:

• chr22-39080377-A-G
• rs34300092
• NM_021822.4:c.172-556A>G

Variant summary

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

The NM_021822.4(APOBEC3G):​c.172-556A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0115 in 215,306 control chromosomes in the GnomAD database, including 56 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 0.016 (56 hom., cov: 31)
  • Exomes 𝑓: 0.0015 (0 hom.)
• Consequence: APOBEC3G NM_021822.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.052 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.172-556A>G		intron	N/A	NP_068594.1
	APOBEC3G	NM_001349436.1		c.139-556A>G		intron	N/A	NP_001336365.1
	APOBEC3G	NM_001349437.2		c.-30-556A>G		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.172-556A>G		intron	N/A	ENSP00000385057.3
	APOBEC3G	ENST00000960612.1		c.172-556A>G		intron	N/A	ENSP00000630671.1
	APOBEC3G	ENST00000851527.1		c.171+1292A>G		intron	N/A	ENSP00000521586.1

Frequencies

GnomAD3 genomes AF: 0.0156 AC: 2378 AN: 152170 Hom.: 56 Cov.: 31

Gnomad AFR AF: 0.0538

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00707

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000323

Gnomad OTH AF: 0.00955

GnomAD4 exome AF: 0.00154 AC: 97 AN: 63018 Hom.: 0 Cov.: 4 AF XY: 0.00145 AC XY: 44 AN XY: 30260

African (AFR) AF: 0.0571 AC: 64 AN: 1120

American (AMR) AF: 0.00435 AC: 2 AN: 460

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 430

East Asian (EAS) AF: 0.00 AC: 0 AN: 308

South Asian (SAS) AF: 0.000814 AC: 1 AN: 1228

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 272

Middle Eastern (MID) AF: 0.0137 AC: 2 AN: 146

European-Non Finnish (NFE) AF: 0.000369 AC: 21 AN: 56910

Other (OTH) AF: 0.00326 AC: 7 AN: 2144

GnomAD4 genome AF: 0.0157 AC: 2388 AN: 152288 Hom.: 56 Cov.: 31 AF XY: 0.0155 AC XY: 1157 AN XY: 74488

African (AFR) AF: 0.0538 AC: 2237 AN: 41548

American (AMR) AF: 0.00706 AC: 108 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000323 AC: 22 AN: 68016

Other (OTH) AF: 0.00945 AC: 20 AN: 2116

Alfa AF: 0.0127 Hom.: 6

Bravo AF: 0.0178

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.71
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism

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: rs34300092; hg19: chr22-39476382;