Genetic Variant APOBEC3H:p.Asn15del (chr22-39100317-TAAC-T) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 1P and 8B. PM4_SupportingBA1

The NM_181773.5(APOBEC3H):c.45_47delCAA(p.Asn15del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 1,612,182 control chromosomes in the GnomAD database, including 91,344 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.33 ( 8404 hom., cov: 0)

Exomes 𝑓: 0.33 ( 82940 hom. )

Consequence

APOBEC3H
NM_181773.5 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.36

Publications

18 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -7 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_181773.5. Strenght limited to Supporting due to length of the change: 1aa.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOBEC3H	NM_181773.5 link	c.45_47delCAA	p.Asn15del	disruptive_inframe_deletion	Exon 2 of 5	ENST00000442487.8	NP_861438.3	Q6NTF7-3B7TQM3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOBEC3H	ENST00000442487.8 link	c.45_47delCAA	p.Asn15del	disruptive_inframe_deletion	Exon 2 of 5	3	NM_181773.5	ENSP00000411754.3		Q6NTF7-3

Frequencies

GnomAD3 genomes

AF:

0.331

AC:

50235

AN:

151596

Hom.:

8393

Cov.:

show subpopulations

Gnomad AFR

AF:

0.322

Gnomad AMI

AF:

0.397

Gnomad AMR

AF:

0.283

Gnomad ASJ

AF:

0.293

Gnomad EAS

AF:

0.274

Gnomad SAS

AF:

0.429

Gnomad FIN

AF:

0.418

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.334

Gnomad OTH

AF:

0.301

GnomAD2 exomes

AF:

0.338

AC:

84816

AN:

251022

AF XY:

0.347

show subpopulations

Gnomad AFR exome

AF:

0.313

Gnomad AMR exome

AF:

0.262

Gnomad ASJ exome

AF:

0.305

Gnomad EAS exome

AF:

0.269

Gnomad FIN exome

AF:

0.422

Gnomad NFE exome

AF:

0.336

Gnomad OTH exome

AF:

0.325

GnomAD4 exome

AF:

0.334

AC:

487150

AN:

1460470

Hom.:

82940

AF XY:

0.338

AC XY:

245352

AN XY:

726438

show subpopulations

African (AFR)

AF:

0.325

AC:

10866

AN:

33472

American (AMR)

AF:

0.265

AC:

11856

AN:

44666

Ashkenazi Jewish (ASJ)

AF:

0.300

AC:

7833

AN:

26114

East Asian (EAS)

AF:

0.267

AC:

10614

AN:

39680

South Asian (SAS)

AF:

0.440

AC:

37939

AN:

86132

European-Finnish (FIN)

AF:

0.422

AC:

22512

AN:

53380

Middle Eastern (MID)

AF:

0.351

AC:

2024

AN:

5762

European-Non Finnish (NFE)

AF:

0.328

AC:

363909

AN:

1110928

Other (OTH)

AF:

0.325

AC:

19597

AN:

60336

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.439

Heterozygous variant carriers

18142

36284

54427

72569

90711

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11780

23560

35340

47120

58900

<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:

0.331

AC:

50282

AN:

151712

Hom.:

8404

Cov.:

AF XY:

0.335

AC XY:

24823

AN XY:

74126

show subpopulations

African (AFR)

AF:

0.323

AC:

13348

AN:

41360

American (AMR)

AF:

0.283

AC:

4309

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.293

AC:

1014

AN:

3466

East Asian (EAS)

AF:

0.274

AC:

1408

AN:

5142

South Asian (SAS)

AF:

0.430

AC:

2067

AN:

4806

European-Finnish (FIN)

AF:

0.418

AC:

4397

AN:

10516

Middle Eastern (MID)

AF:

0.316

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.334

AC:

22661

AN:

67864

Other (OTH)

AF:

0.296

AC:

625

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

1674

3348

5022

6696

8370

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

526

1052

1578

2104

2630

<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:

0.330

Hom.:

1522

Bravo

AF:

0.316

Asia WGS

AF:

0.322

AC:

1127

AN:

3478

EpiCase

AF:

0.326

EpiControl

AF:

0.324

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.4

Mutation Taster

=82/18

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

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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