dbSNP rs139316: APOBEC3H:c.*61T>C (chr22-39103758-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.*61T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 1,595,670 control chromosomes in the GnomAD database, including 182,067 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 0.54 ( 23615 hom., cov: 31)

Exomes 𝑓: 0.46 ( 158452 hom. )

Consequence

APOBEC3H
NM_181773.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0580

Publications

36 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOBEC3H	NM_181773.5 link	c.*61T>C		3_prime_UTR_variant	Exon 5 of 5	ENST00000442487.8	NP_861438.3	Q6NTF7-3B7TQM3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
APOBEC3H	ENST00000442487.8 link	c.*61T>C	3_prime_UTR_variant	Exon 5 of 5	3	NM_181773.5	ENSP00000411754.3	Q6NTF7-3
APOBEC3H	ENST00000348946.8 link	c.*61T>C	3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000216123.5	Q6NTF7-2
APOBEC3H	ENST00000401756.5 link	c.*104T>C	3_prime_UTR_variant	Exon 6 of 6	3		ENSP00000385741.1	Q6NTF7-1

Frequencies

GnomAD3 genomes

AF:

0.539

AC:

81924

AN:

151896

Hom.:

23587

Cov.:

show subpopulations

Gnomad AFR

AF:

0.760

Gnomad AMI

AF:

0.525

Gnomad AMR

AF:

0.391

Gnomad ASJ

AF:

0.456

Gnomad EAS

AF:

0.354

Gnomad SAS

AF:

0.475

Gnomad FIN

AF:

0.537

Gnomad MID

AF:

0.456

Gnomad NFE

AF:

0.464

Gnomad OTH

AF:

0.488

GnomAD4 exome

AF:

0.463

AC:

668026

AN:

1443656

Hom.:

158452

Cov.:

AF XY:

0.463

AC XY:

333396

AN XY:

719346

show subpopulations

African (AFR)

AF:

0.772

AC:

25488

AN:

33012

American (AMR)

AF:

0.321

AC:

14346

AN:

44698

Ashkenazi Jewish (ASJ)

AF:

0.457

AC:

11892

AN:

26030

East Asian (EAS)

AF:

0.337

AC:

13371

AN:

39632

South Asian (SAS)

AF:

0.488

AC:

41887

AN:

85852

European-Finnish (FIN)

AF:

0.544

AC:

29047

AN:

53398

Middle Eastern (MID)

AF:

0.489

AC:

2803

AN:

5732

European-Non Finnish (NFE)

AF:

0.458

AC:

501403

AN:

1095518

Other (OTH)

AF:

0.465

AC:

27789

AN:

59784

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

17757

35514

53270

71027

88784

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.539

AC:

82006

AN:

152014

Hom.:

23615

Cov.:

AF XY:

0.537

AC XY:

39935

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.760

AC:

31510

AN:

41478

American (AMR)

AF:

0.390

AC:

5954

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.456

AC:

1580

AN:

3464

East Asian (EAS)

AF:

0.355

AC:

1831

AN:

5162

South Asian (SAS)

AF:

0.476

AC:

2296

AN:

4824

European-Finnish (FIN)

AF:

0.537

AC:

5670

AN:

10560

Middle Eastern (MID)

AF:

0.463

AC:

136

AN:

294

European-Non Finnish (NFE)

AF:

0.464

AC:

31531

AN:

67952

Other (OTH)

AF:

0.484

AC:

1020

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1764

3529

5293

7058

8822

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.482

Hom.:

71600

Bravo

AF:

0.534

Asia WGS

AF:

0.406

AC:

1418

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

3.7

(source)

DANN

Benign

0.40

PhyloP100

0.058

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

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rs139316

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