chr22-39085182-C-T

Position:

• chr22-39085182-C-T

Variant summary

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

The NM_021822.4(APOBEC3G):​c.736-1097C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 152,130 control chromosomes in the GnomAD database, including 17,341 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 0.44 (17341 hom., cov: 32)
• Consequence: APOBEC3G NM_021822.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOBEC3G	NM_021822.4	c.736-1097C>T		intron_variant		ENST00000407997.4	NP_068594.1
APOBEC3G	NM_001349436.1	c.703-1097C>T		intron_variant			NP_001336365.1
APOBEC3G	NM_001349437.2	c.535-1097C>T		intron_variant			NP_001336366.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOBEC3G	ENST00000407997.4	c.736-1097C>T		intron_variant		1	NM_021822.4	ENSP00000385057.3

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67293 AN: 152012 Hom.: 17335 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.442 AC: 67306 AN: 152130 Hom.: 17341 Cov.: 32 AF XY: 0.444 AC XY: 33048 AN XY: 74366

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.498

Alfa AF: 0.531 Hom.: 35702

Bravo AF: 0.441

Asia WGS AF: 0.610 AC: 2118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.22

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: rs2413570; hg19: chr22-39481187;