rs139279

Variant names:

• chr22-39098079-C-G
• rs139279
• NM_181773.5:c.-8+736C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181773.5(APOBEC3H):​c.-8+736C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,866 control chromosomes in the GnomAD database, including 13,019 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 0.41 (13019 hom., cov: 32)
• Consequence: APOBEC3H NM_181773.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626
• Publications: 3 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOBEC3H	NM_181773.5	c.-8+736C>G		intron_variant	Intron 1 of 4	ENST00000442487.8	NP_861438.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOBEC3H	ENST00000442487.8	c.-8+736C>G		intron_variant	Intron 1 of 4	3	NM_181773.5	ENSP00000411754.3

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61687 AN: 151748 Hom.: 12992 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.351

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.407 AC: 61770 AN: 151866 Hom.: 13019 Cov.: 32 AF XY: 0.410 AC XY: 30402 AN XY: 74224

African (AFR) AF: 0.516 AC: 21373 AN: 41450

American (AMR) AF: 0.322 AC: 4915 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3468

East Asian (EAS) AF: 0.345 AC: 1781 AN: 5160

South Asian (SAS) AF: 0.456 AC: 2194 AN: 4816

European-Finnish (FIN) AF: 0.455 AC: 4781 AN: 10510

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.360 AC: 24423 AN: 67900

Other (OTH) AF: 0.347 AC: 733 AN: 2110

Alfa AF: 0.386 Hom.: 1465

Bravo AF: 0.397

Asia WGS AF: 0.370 AC: 1294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.49
PhyloP100		0.63
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs139279; hg19: chr22-39494084;