rs139279

Positions:

• chr22-39098079-C-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
APOBEC3H	NM_181773.5	c.-8+736C>G		intron_variant		ENST00000442487.8	NP_861438.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOBEC3H	ENST00000442487.8	c.-8+736C>G		intron_variant		3	NM_181773.5	ENSP00000411754	A2

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

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.347

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

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

Other links and lift over

dbSNP: rs139279; hg19: chr22-39494084;