Variant 22-39101399-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_181773.5(APOBEC3H):c.313G>C(p.Gly105Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 1,610,706 control chromosomes in the GnomAD database, including 187,811 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.56 ( 25134 hom., cov: 22)

Exomes 𝑓: 0.47 ( 162677 hom. )

Consequence

APOBEC3H
NM_181773.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.65

Variant links:

Genes affected

APOBEC3H (HGNC:24100): (apolipoprotein B mRNA editing enzyme catalytic subunit 3H) This gene encodes a member of the apolipoprotein B mRNA-editing enzyme catalytic polypeptide 3 family of proteins. The encoded protein is a cytidine deaminase that has antiretroviral activity by generating lethal hypermutations in viral genomes. Polymorphisms and alternative splicing in this gene influence its antiretroviral activity and are associated with increased resistence to human immunodeficiency virus type 1 infection in certain populations. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Oct 2009]

APOBEC3H links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.6928052E-6).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOBEC3H	NM_181773.5 linkuse as main transcript	c.313G>C	p.Gly105Arg	missense_variant	3/5	ENST00000442487.8	NP_861438.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOBEC3H	ENST00000442487.8 linkuse as main transcript	c.313G>C	p.Gly105Arg	missense_variant	3/5	3	NM_181773.5	ENSP00000411754	A2	Q6NTF7-3

Frequencies

GnomAD3 genomes

AF:

0.558

AC:

83026

AN:

148862

Hom.:

25099

Cov.:

show subpopulations

Gnomad AFR

AF:

0.816

Gnomad AMI

AF:

0.527

Gnomad AMR

AF:

0.418

Gnomad ASJ

AF:

0.455

Gnomad EAS

AF:

0.335

Gnomad SAS

AF:

0.474

Gnomad FIN

AF:

0.541

Gnomad MID

AF:

0.474

Gnomad NFE

AF:

0.465

Gnomad OTH

AF:

0.502

GnomAD3 exomes

AF:

0.470

AC:

117985

AN:

251172

Hom.:

29398

AF XY:

0.470

AC XY:

63853

AN XY:

135800

show subpopulations

Gnomad AFR exome

AF:

0.819

Gnomad AMR exome

AF:

0.345

Gnomad ASJ exome

AF:

0.457

Gnomad EAS exome

AF:

0.321

Gnomad SAS exome

AF:

0.487

Gnomad FIN exome

AF:

0.544

Gnomad NFE exome

AF:

0.465

Gnomad OTH exome

AF:

0.453

GnomAD4 exome

AF:

0.465

AC:

680340

AN:

1461740

Hom.:

162677

Cov.:

AF XY:

0.466

AC XY:

338653

AN XY:

727180

show subpopulations

Gnomad4 AFR exome

AF:

0.829

Gnomad4 AMR exome

AF:

0.353

Gnomad4 ASJ exome

AF:

0.456

Gnomad4 EAS exome

AF:

0.318

Gnomad4 SAS exome

AF:

0.488

Gnomad4 FIN exome

AF:

0.544

Gnomad4 NFE exome

AF:

0.459

Gnomad4 OTH exome

AF:

0.470

GnomAD4 genome

AF:

0.558

AC:

83112

AN:

148966

Hom.:

25134

Cov.:

AF XY:

0.556

AC XY:

40337

AN XY:

72512

show subpopulations

Gnomad4 AFR

AF:

0.816

Gnomad4 AMR

AF:

0.417

Gnomad4 ASJ

AF:

0.455

Gnomad4 EAS

AF:

0.335

Gnomad4 SAS

AF:

0.475

Gnomad4 FIN

AF:

0.541

Gnomad4 NFE

AF:

0.465

Gnomad4 OTH

AF:

0.498

Alfa

AF:

0.436

Hom.:

4607

Bravo

AF:

0.554

TwinsUK

AF:

0.461

AC:

1710

ALSPAC

AF:

0.455

AC:

1755

ESP6500AA

AF:

0.811

AC:

3573

ESP6500EA

AF:

0.461

AC:

3964

ExAC

AF:

0.481

AC:

58450

Asia WGS

AF:

0.388

AC:

1275

AN:

3278

EpiCase

AF:

0.457

EpiControl

AF:

0.454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.055

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.67

CADD

Benign

0.0010

DANN

Benign

0.16

DEOGEN2

Benign

0.0027

.;T;.;T;.;.

Eigen

Benign

-2.0

Eigen_PC

Benign

-1.9

FATHMM_MKL

Benign

0.00079

LIST_S2

Benign

0.052

T;T;T;.;T;.

MetaRNN

Benign

0.0000017

T;T;T;T;T;T

MetaSVM

Benign

-0.97

MutationAssessor

Benign

-2.6

.;N;N;N;N;.

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Benign

0.23

PROVEAN

Benign

3.4

N;.;N;N;N;.

REVEL

Benign

0.068

Sift

Benign

1.0

T;.;T;T;T;.

Sift4G

Benign

1.0

T;T;T;T;T;T

Vest4

0.051

MPC

0.22

ClinPred

0.0081

GERP RS

-4.6

Varity_R

0.13

gMVP

0.13

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