rs139316

Variant names:

• chr22-39103758-T-C
• rs139316
• NM_181773.5:c.*61T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001166003.3(APOBEC3H):​c.*104T>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_001166003.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 36 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001166003.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOBEC3H	NM_181773.5	MANE Select	c.*61T>C		3_prime_UTR	Exon 5 of 5	NP_861438.3
	APOBEC3H	NM_001166003.3		c.*104T>C		3_prime_UTR	Exon 6 of 6	NP_001159475.2
	APOBEC3H	NM_001166002.3		c.*61T>C		3_prime_UTR	Exon 5 of 5	NP_001159474.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOBEC3H	ENST00000442487.8	TSL:3 MANE Select	c.*61T>C		3_prime_UTR	Exon 5 of 5	ENSP00000411754.3
	APOBEC3H	ENST00000348946.8	TSL:1	c.*61T>C		3_prime_UTR	Exon 5 of 5	ENSP00000216123.5
	APOBEC3H	ENST00000401756.5	TSL:3	c.*104T>C		3_prime_UTR	Exon 6 of 6	ENSP00000385741.1

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

African (AFR) AF: 0.772 AC: 25488 AN: 33012

American (AMR) AF: 0.321 AC: 14346 AN: 44698

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 11892 AN: 26030

East Asian (EAS) AF: 0.337 AC: 13371 AN: 39632

South Asian (SAS) AF: 0.488 AC: 41887 AN: 85852

European-Finnish (FIN) AF: 0.544 AC: 29047 AN: 53398

Middle Eastern (MID) AF: 0.489 AC: 2803 AN: 5732

European-Non Finnish (NFE) AF: 0.458 AC: 501403 AN: 1095518

Other (OTH) AF: 0.465 AC: 27789 AN: 59784

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

African (AFR) AF: 0.760 AC: 31510 AN: 41478

American (AMR) AF: 0.390 AC: 5954 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1580 AN: 3464

East Asian (EAS) AF: 0.355 AC: 1831 AN: 5162

South Asian (SAS) AF: 0.476 AC: 2296 AN: 4824

European-Finnish (FIN) AF: 0.537 AC: 5670 AN: 10560

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31531 AN: 67952

Other (OTH) AF: 0.484 AC: 1020 AN: 2108

Alfa AF: 0.482 Hom.: 71600

Bravo AF: 0.534

Asia WGS AF: 0.406 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.7
DANN	Benign	0.40
PhyloP100		0.058
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: rs139316; hg19: chr22-39499763; COSMIC: COSV62378777; COSMIC: COSV62378777;