Genetic Variant APOBEC3H:c.544-90T>C (chr22-39103599-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_181773.5(APOBEC3H):c.544-90T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 1,396,454 control chromosomes in the GnomAD database, including 74,710 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 0.33 ( 8292 hom., cov: 33)

Exomes 𝑓: 0.32 ( 66418 hom. )

Consequence

APOBEC3H
NM_181773.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0970

Publications

16 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOBEC3H	NM_181773.5 link	c.544-90T>C		intron_variant	Intron 4 of 4	ENST00000442487.8	NP_861438.3	Q6NTF7-3B7TQM3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
APOBEC3H	ENST00000442487.8 link	c.544-90T>C	intron_variant	Intron 4 of 4	3	NM_181773.5	ENSP00000411754.3	Q6NTF7-3
APOBEC3H	ENST00000348946.8 link	c.544-93T>C	intron_variant	Intron 4 of 4	1		ENSP00000216123.5	Q6NTF7-2
APOBEC3H	ENST00000401756.5 link	c.*35-90T>C	intron_variant	Intron 5 of 5	3		ENSP00000385741.1	Q6NTF7-1

Frequencies

GnomAD3 genomes

AF:

0.328

AC:

49888

AN:

152024

Hom.:

8284

Cov.:

show subpopulations

Gnomad AFR

AF:

0.319

Gnomad AMI

AF:

0.400

Gnomad AMR

AF:

0.265

Gnomad ASJ

AF:

0.293

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.425

Gnomad FIN

AF:

0.420

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.333

Gnomad OTH

AF:

0.296

GnomAD4 exome

AF:

0.322

AC:

400435

AN:

1244312

Hom.:

66418

AF XY:

0.328

AC XY:

206214

AN XY:

629604

show subpopulations

African (AFR)

AF:

0.314

AC:

8844

AN:

28210

American (AMR)

AF:

0.238

AC:

10541

AN:

44358

Ashkenazi Jewish (ASJ)

AF:

0.297

AC:

7359

AN:

24790

East Asian (EAS)

AF:

0.256

AC:

9919

AN:

38724

South Asian (SAS)

AF:

0.434

AC:

35393

AN:

81620

European-Finnish (FIN)

AF:

0.421

AC:

22336

AN:

53014

Middle Eastern (MID)

AF:

0.340

AC:

1756

AN:

5162

European-Non Finnish (NFE)

AF:

0.314

AC:

287619

AN:

915250

Other (OTH)

AF:

0.313

AC:

16668

AN:

53184

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

12477

24955

37432

49910

62387

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8420

16840

25260

33680

42100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.328

AC:

49932

AN:

152142

Hom.:

8292

Cov.:

AF XY:

0.332

AC XY:

24675

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.319

AC:

13229

AN:

41494

American (AMR)

AF:

0.265

AC:

4047

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.293

AC:

1015

AN:

3466

East Asian (EAS)

AF:

0.269

AC:

1393

AN:

5172

South Asian (SAS)

AF:

0.426

AC:

2054

AN:

4818

European-Finnish (FIN)

AF:

0.420

AC:

4446

AN:

10592

Middle Eastern (MID)

AF:

0.320

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.333

AC:

22675

AN:

67992

Other (OTH)

AF:

0.291

AC:

616

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1696

3392

5088

6784

8480

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

524

1048

1572

2096

2620

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.325

Hom.:

20175

Bravo

AF:

0.311

Asia WGS

AF:

0.321

AC:

1119

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.3

(source)

DANN

Benign

0.68

PhyloP100

-0.097

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over