rs139317

Variant names:

• chr22-39103897-C-T
• rs139317
• NM_181773.5:c.*200C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 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=-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 rank	MANE	Protein	UniProt
APOBEC3H	NM_181773.5	c.*200C>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000442487.8	NP_861438.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOBEC3H	ENST00000442487.8	c.*200C>T		3_prime_UTR_variant	Exon 5 of 5	3	NM_181773.5	ENSP00000411754.3
APOBEC3H	ENST00000348946.8	c.*200C>T		3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000216123.5
APOBEC3H	ENST00000401756.5	c.*243C>T		3_prime_UTR_variant	Exon 6 of 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

African (AFR) AF: 0.821 AC: 10812 AN: 13174

American (AMR) AF: 0.349 AC: 7072 AN: 20260

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 6285 AN: 13734

East Asian (EAS) AF: 0.339 AC: 11111 AN: 32788

South Asian (SAS) AF: 0.487 AC: 21574 AN: 44338

European-Finnish (FIN) AF: 0.543 AC: 20059 AN: 36916

Middle Eastern (MID) AF: 0.489 AC: 1554 AN: 3178

European-Non Finnish (NFE) AF: 0.459 AC: 126366 AN: 275150

Other (OTH) AF: 0.475 AC: 12492 AN: 26314

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

African (AFR) AF: 0.824 AC: 34205 AN: 41488

American (AMR) AF: 0.399 AC: 6096 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1583 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1837 AN: 5178

South Asian (SAS) AF: 0.477 AC: 2301 AN: 4828

European-Finnish (FIN) AF: 0.537 AC: 5670 AN: 10566

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31555 AN: 67968

Other (OTH) AF: 0.496 AC: 1048 AN: 2112

Alfa AF: 0.483 Hom.: 36858

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
PhyloP100		-0.92
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: rs139317; hg19: chr22-39499902;