rs139283

chr22-39099579-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.-7-693C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 152,104 control chromosomes in the GnomAD database, including 26,448 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 0.56 (26448 hom., cov: 32)
• Consequence: APOBEC3H NM_181773.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOBEC3H	NM_181773.5	c.-7-693C>G		intron_variant		ENST00000442487.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOBEC3H	ENST00000442487.8	c.-7-693C>G		intron_variant		3	NM_181773.5	A2

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85544 AN: 151986 Hom.: 26394 Cov.: 32

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.563 AC: 85655 AN: 152104 Hom.: 26448 Cov.: 32 AF XY: 0.561 AC XY: 41695 AN XY: 74354

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.501

Alfa AF: 0.525 Hom.: 2838

Bravo AF: 0.563

Asia WGS AF: 0.417 AC: 1456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.7
Dann	Benign	0.66

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: rs139283; hg19: chr22-39495584;