rs139316

chr22-39103758-T-C

Variant summary

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

The NM_181773.5(APOBEC3H):c.*61T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 1,595,670 control chromosomes in the GnomAD database, including 182,067 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 0.54 (23615 hom., cov: 31)
  • Exomes 𝑓: 0.46 (158452 hom.)
• Consequence: APOBEC3H NM_181773.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOBEC3H	NM_181773.5	c.*61T>C		3_prime_UTR_variant	5/5	ENST00000442487.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOBEC3H	ENST00000442487.8	c.*61T>C		3_prime_UTR_variant	5/5	3	NM_181773.5	A2
APOBEC3H	ENST00000348946.8	c.*61T>C		3_prime_UTR_variant	5/5	1		A2
APOBEC3H	ENST00000401756.5	c.*104T>C		3_prime_UTR_variant	6/6	3		P2

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81924 AN: 151896 Hom.: 23587 Cov.: 31

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.488

GnomAD4 exome AF: 0.463 AC: 668026 AN: 1443656 Hom.: 158452 Cov.: 31 AF XY: 0.463 AC XY: 333396 AN XY: 719346

Gnomad4 AFR exome AF: 0.772

Gnomad4 AMR exome AF: 0.321

Gnomad4 ASJ exome AF: 0.457

Gnomad4 EAS exome AF: 0.337

Gnomad4 SAS exome AF: 0.488

Gnomad4 FIN exome AF: 0.544

Gnomad4 NFE exome AF: 0.458

Gnomad4 OTH exome AF: 0.465

GnomAD4 genome AF: 0.539 AC: 82006 AN: 152014 Hom.: 23615 Cov.: 31 AF XY: 0.537 AC XY: 39935 AN XY: 74300

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.484

Alfa AF: 0.465 Hom.: 32707

Bravo AF: 0.534

Asia WGS AF: 0.406 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.7
Dann	Benign	0.40

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: rs139316; hg19: chr22-39499763; COSMIC: COSV62378777; COSMIC: COSV62378777;