rs139317

Positions:

• chr22-39103897-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181773.5(APOBEC3H):​c.*200C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 617,942 control chromosomes in the GnomAD database, including 78,427 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 (25858 hom., cov: 32)
  • Exomes 𝑓: 0.47 (52569 hom.)
• Consequence: APOBEC3H NM_181773.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.919

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOBEC3H	NM_181773.5	c.*200C>T		3_prime_UTR_variant	5/5	ENST00000442487.8	NP_861438.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOBEC3H	ENST00000442487.8	c.*200C>T		3_prime_UTR_variant	5/5	3	NM_181773.5	ENSP00000411754.3
APOBEC3H	ENST00000348946.8	c.*200C>T		3_prime_UTR_variant	5/5	1		ENSP00000216123.5
APOBEC3H	ENST00000401756.5	c.*243C>T		3_prime_UTR_variant	6/6	3		ENSP00000385741.1

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84816 AN: 151972 Hom.: 25815 Cov.: 32

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.501

GnomAD4 exome AF: 0.467 AC: 217325 AN: 465852 Hom.: 52569 Cov.: 5 AF XY: 0.466 AC XY: 115580 AN XY: 248000

Gnomad4 AFR exome AF: 0.821

Gnomad4 AMR exome AF: 0.349

Gnomad4 ASJ exome AF: 0.458

Gnomad4 EAS exome AF: 0.339

Gnomad4 SAS exome AF: 0.487

Gnomad4 FIN exome AF: 0.543

Gnomad4 NFE exome AF: 0.459

Gnomad4 OTH exome AF: 0.475

GnomAD4 genome AF: 0.558 AC: 84915 AN: 152090 Hom.: 25858 Cov.: 32 AF XY: 0.556 AC XY: 41310 AN XY: 74336

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.496

Alfa AF: 0.475 Hom.: 25747

Bravo AF: 0.555

Asia WGS AF: 0.413 AC: 1439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.52

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: rs139317; hg19: chr22-39499902;