Variant 22-39100331-G-T 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.53G>T(p.Arg18Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 1,612,954 control chromosomes in the GnomAD database, including 61,402 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 0.23 ( 4513 hom., cov: 31)

Exomes 𝑓: 0.27 ( 56889 hom. )

Consequence

APOBEC3H
NM_181773.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.116

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:

APOBEC3H (HGNC:):

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=0.005291611).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.318 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.53G>T	p.Arg18Leu	missense_variant	2/5	ENST00000442487.8	NP_861438.3	Q6NTF7-3B7TQM3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOBEC3H	ENST00000442487.8 linkuse as main transcript	c.53G>T	p.Arg18Leu	missense_variant	2/5	3	NM_181773.5	ENSP00000411754.3		Q6NTF7-3

Frequencies

GnomAD3 genomes

AF:

0.226

AC:

34298

AN:

151816

Hom.:

4511

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0858

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.228

Gnomad ASJ

AF:

0.257

Gnomad EAS

AF:

0.161

Gnomad SAS

AF:

0.330

Gnomad FIN

AF:

0.375

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.282

Gnomad OTH

AF:

0.211

GnomAD3 exomes

AF:

0.268

AC:

67324

AN:

251224

Hom.:

9769

AF XY:

0.279

AC XY:

37821

AN XY:

135802

show subpopulations

Gnomad AFR exome

AF:

0.0777

Gnomad AMR exome

AF:

0.224

Gnomad ASJ exome

AF:

0.269

Gnomad EAS exome

AF:

0.158

Gnomad SAS exome

AF:

0.343

Gnomad FIN exome

AF:

0.377

Gnomad NFE exome

AF:

0.285

Gnomad OTH exome

AF:

0.268

GnomAD4 exome

AF:

0.274

AC:

399780

AN:

1461020

Hom.:

56889

Cov.:

AF XY:

0.277

AC XY:

201362

AN XY:

726738

show subpopulations

Gnomad4 AFR exome

AF:

0.0764

Gnomad4 AMR exome

AF:

0.224

Gnomad4 ASJ exome

AF:

0.265

Gnomad4 EAS exome

AF:

0.143

Gnomad4 SAS exome

AF:

0.346

Gnomad4 FIN exome

AF:

0.376

Gnomad4 NFE exome

AF:

0.277

Gnomad4 OTH exome

AF:

0.257

GnomAD4 genome

AF:

0.226

AC:

34304

AN:

151934

Hom.:

4513

Cov.:

AF XY:

0.231

AC XY:

17115

AN XY:

74236

show subpopulations

Gnomad4 AFR

AF:

0.0856

Gnomad4 AMR

AF:

0.227

Gnomad4 ASJ

AF:

0.257

Gnomad4 EAS

AF:

0.161

Gnomad4 SAS

AF:

0.332

Gnomad4 FIN

AF:

0.375

Gnomad4 NFE

AF:

0.282

Gnomad4 OTH

AF:

0.207

Alfa

AF:

0.234

Hom.:

1481

Bravo

AF:

0.205

TwinsUK

AF:

0.268

AC:

992

ALSPAC

AF:

0.273

AC:

1053

ESP6500AA

AF:

0.0828

AC:

365

ESP6500EA

AF:

0.274

AC:

2353

ExAC

AF:

0.268

AC:

32578

Asia WGS

AF:

0.222

AC:

775

AN:

3478

EpiCase

AF:

0.273

EpiControl

AF:

0.269

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.19

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.018

.;T;.;T;.;.

Eigen

Benign

-0.66

Eigen_PC

Benign

-0.92

FATHMM_MKL

Benign

0.019

LIST_S2

Benign

0.49

T;T;T;.;T;.

MetaRNN

Benign

0.0053

T;T;T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.8

.;L;L;L;L;.

PrimateAI

Benign

0.34

PROVEAN

Benign

-2.2

N;.;N;N;N;.

REVEL

Benign

0.12

Sift

Benign

0.14

T;.;T;T;T;.

Sift4G

Uncertain

0.031

D;D;D;D;D;D

Vest4

0.18

MPC

0.47

ClinPred

0.012

GERP RS

-0.21

Varity_R

0.25

gMVP

0.37

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