Variant 22-39081118-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000407997.4(APOBEC3G):c.357T>C(p.Phe119=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 1,614,034 control chromosomes in the GnomAD database, including 136,188 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 0.31 ( 9178 hom., cov: 32)

Exomes 𝑓: 0.41 ( 127010 hom. )

Consequence

APOBEC3G
ENST00000407997.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.40

Variant links:

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]

APOBEC3G links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP7

Synonymous conserved (PhyloP=-2.4 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOBEC3G	NM_021822.4 linkuse as main transcript	c.357T>C	p.Phe119=	synonymous_variant	3/8	ENST00000407997.4	NP_068594.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOBEC3G	ENST00000407997.4 linkuse as main transcript	c.357T>C	p.Phe119=	synonymous_variant	3/8	1	NM_021822.4	ENSP00000385057	P1	Q9HC16-1

Frequencies

GnomAD3 genomes

AF:

0.314

AC:

47743

AN:

152058

Hom.:

9181

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0845

Gnomad AMI

AF:

0.384

Gnomad AMR

AF:

0.411

Gnomad ASJ

AF:

0.448

Gnomad EAS

AF:

0.231

Gnomad SAS

AF:

0.419

Gnomad FIN

AF:

0.291

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.424

Gnomad OTH

AF:

0.379

GnomAD3 exomes

AF:

0.374

AC:

93928

AN:

251462

Hom.:

18886

AF XY:

0.386

AC XY:

52440

AN XY:

135904

show subpopulations

Gnomad AFR exome

AF:

0.0740

Gnomad AMR exome

AF:

0.383

Gnomad ASJ exome

AF:

0.455

Gnomad EAS exome

AF:

0.228

Gnomad SAS exome

AF:

0.434

Gnomad FIN exome

AF:

0.287

Gnomad NFE exome

AF:

0.428

Gnomad OTH exome

AF:

0.410

GnomAD4 exome

AF:

0.410

AC:

599417

AN:

1461858

Hom.:

127010

Cov.:

AF XY:

0.412

AC XY:

299924

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.0691

Gnomad4 AMR exome

AF:

0.384

Gnomad4 ASJ exome

AF:

0.450

Gnomad4 EAS exome

AF:

0.244

Gnomad4 SAS exome

AF:

0.433

Gnomad4 FIN exome

AF:

0.290

Gnomad4 NFE exome

AF:

0.431

Gnomad4 OTH exome

AF:

0.396

GnomAD4 genome

AF:

0.314

AC:

47720

AN:

152176

Hom.:

9178

Cov.:

AF XY:

0.312

AC XY:

23211

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.0842

Gnomad4 AMR

AF:

0.411

Gnomad4 ASJ

AF:

0.448

Gnomad4 EAS

AF:

0.231

Gnomad4 SAS

AF:

0.419

Gnomad4 FIN

AF:

0.291

Gnomad4 NFE

AF:

0.424

Gnomad4 OTH

AF:

0.376

Alfa

AF:

0.409

Hom.:

26760

Bravo

AF:

0.310

Asia WGS

AF:

0.301

AC:

1047

AN:

3478

EpiCase

AF:

0.444

EpiControl

AF:

0.451

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.8

DANN

Benign

0.51

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over