Variant rs139302 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.534G>C(p.Glu178Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 1,610,556 control chromosomes in the GnomAD database, including 186,293 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 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 0.55 ( 24656 hom., cov: 29)

Exomes 𝑓: 0.46 ( 161637 hom. )

Consequence

APOBEC3H
NM_181773.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.31

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=8.9006903E-7).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOBEC3H	NM_181773.5 linkuse as main transcript	c.534G>C	p.Glu178Asp	missense_variant	4/5	ENST00000442487.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOBEC3H	ENST00000442487.8 linkuse as main transcript	c.534G>C	p.Glu178Asp	missense_variant	4/5	3	NM_181773.5	A2	Q6NTF7-3

Frequencies

GnomAD3 genomes

AF:

0.549

AC:

83242

AN:

151702

Hom.:

24626

Cov.:

show subpopulations

Gnomad AFR

AF:

0.793

Gnomad AMI

AF:

0.526

Gnomad AMR

AF:

0.396

Gnomad ASJ

AF:

0.457

Gnomad EAS

AF:

0.354

Gnomad SAS

AF:

0.474

Gnomad FIN

AF:

0.536

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.464

Gnomad OTH

AF:

0.493

GnomAD3 exomes

AF:

0.465

AC:

114404

AN:

246284

Hom.:

28678

AF XY:

0.466

AC XY:

62080

AN XY:

133134

show subpopulations

Gnomad AFR exome

AF:

0.799

Gnomad AMR exome

AF:

0.312

Gnomad ASJ exome

AF:

0.458

Gnomad EAS exome

AF:

0.339

Gnomad SAS exome

AF:

0.487

Gnomad FIN exome

AF:

0.544

Gnomad NFE exome

AF:

0.464

Gnomad OTH exome

AF:

0.449

GnomAD4 exome

AF:

0.464

AC:

677249

AN:

1458734

Hom.:

161637

Cov.:

AF XY:

0.465

AC XY:

337182

AN XY:

725518

show subpopulations

Gnomad4 AFR exome

AF:

0.806

Gnomad4 AMR exome

AF:

0.322

Gnomad4 ASJ exome

AF:

0.457

Gnomad4 EAS exome

AF:

0.337

Gnomad4 SAS exome

AF:

0.487

Gnomad4 FIN exome

AF:

0.544

Gnomad4 NFE exome

AF:

0.458

Gnomad4 OTH exome

AF:

0.467

GnomAD4 genome

AF:

0.549

AC:

83327

AN:

151822

Hom.:

24656

Cov.:

AF XY:

0.546

AC XY:

40547

AN XY:

74198

show subpopulations

Gnomad4 AFR

AF:

0.793

Gnomad4 AMR

AF:

0.395

Gnomad4 ASJ

AF:

0.457

Gnomad4 EAS

AF:

0.354

Gnomad4 SAS

AF:

0.475

Gnomad4 FIN

AF:

0.536

Gnomad4 NFE

AF:

0.464

Gnomad4 OTH

AF:

0.488

Alfa

AF:

0.468

Hom.:

12863

Bravo

AF:

0.544

TwinsUK

AF:

0.461

AC:

1711

ALSPAC

AF:

0.456

AC:

1756

ESP6500AA

AF:

0.786

AC:

3461

ESP6500EA

AF:

0.461

AC:

3964

ExAC

AF:

0.477

AC:

57868

Asia WGS

AF:

0.407

AC:

1417

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.63

Cadd

Benign

0.080

Dann

Benign

0.46

DEOGEN2

Benign

0.011

T;.;T;.

Eigen

Benign

-2.0

Eigen_PC

Benign

-2.1

FATHMM_MKL

Benign

0.0079

LIST_S2

Benign

0.27

T;T;.;T

MetaRNN

Benign

8.9e-7

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.59

N;N;N;N

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Benign

0.26

Sift4G

Benign

0.62

T;T;T;T

Vest4

0.036

MutPred

0.30

Loss of methylation at K174 (P = 0.1316);Loss of methylation at K174 (P = 0.1316);Loss of methylation at K174 (P = 0.1316);Loss of methylation at K174 (P = 0.1316);

MPC

0.17

ClinPred

0.0085

GERP RS

-6.1

Varity_R

0.062

gMVP

0.36

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