rs139292

Variant names:

• chr22-39100317-TAAC-T
• rs139292
• NM_181773.5:c.45_47delCAA

Your query was ambiguous. Multiple possible variants found:

• chr22-39100317-TAAC-T
• chr22-39100317-TAAC-TAACAAC

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 1P and 8B. PM4_Supporting BA1

The NM_001166003.3(APOBEC3H):​c.45_47delCAA​(p.Asn15del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 1,612,182 control chromosomes in the GnomAD database, including 91,344 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.33 (8404 hom., cov: 0)
  • Exomes 𝑓: 0.33 (82940 hom.)
• Consequence: APOBEC3H NM_001166003.3 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• 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 -7 ACMG points.

• PM4: Nonframeshift variant in NON repetitive region in NM_001166003.3. Strenght limited to Supporting due to length of the change: 1aa.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.415 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOBEC3H	NM_181773.5	MANE Select	c.45_47delCAA	p.Asn15del	disruptive_inframe_deletion	Exon 2 of 5	NP_861438.3
	APOBEC3H	NM_001166003.3		c.45_47delCAA	p.Asn15del	disruptive_inframe_deletion	Exon 2 of 6	NP_001159475.2
	APOBEC3H	NM_001166002.3		c.45_47delCAA	p.Asn15del	disruptive_inframe_deletion	Exon 2 of 5	NP_001159474.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOBEC3H	ENST00000442487.8	TSL:3 MANE Select	c.45_47delCAA	p.Asn15del	disruptive_inframe_deletion	Exon 2 of 5	ENSP00000411754.3
	APOBEC3H	ENST00000348946.8	TSL:1	c.45_47delCAA	p.Asn15del	disruptive_inframe_deletion	Exon 2 of 5	ENSP00000216123.5
	APOBEC3H	ENST00000613996.1	TSL:1	c.45_47delCAA	p.Asn15del	disruptive_inframe_deletion	Exon 1 of 3	ENSP00000482682.1

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50235 AN: 151596 Hom.: 8393 Cov.: 0

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.301

GnomAD2 exomes AF: 0.338 AC: 84816 AN: 251022 AF XY: 0.347

Gnomad AFR exome AF: 0.313

Gnomad AMR exome AF: 0.262

Gnomad ASJ exome AF: 0.305

Gnomad EAS exome AF: 0.269

Gnomad FIN exome AF: 0.422

Gnomad NFE exome AF: 0.336

Gnomad OTH exome AF: 0.325

GnomAD4 exome AF: 0.334 AC: 487150 AN: 1460470 Hom.: 82940 AF XY: 0.338 AC XY: 245352 AN XY: 726438

African (AFR) AF: 0.325 AC: 10866 AN: 33472

American (AMR) AF: 0.265 AC: 11856 AN: 44666

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 7833 AN: 26114

East Asian (EAS) AF: 0.267 AC: 10614 AN: 39680

South Asian (SAS) AF: 0.440 AC: 37939 AN: 86132

European-Finnish (FIN) AF: 0.422 AC: 22512 AN: 53380

Middle Eastern (MID) AF: 0.351 AC: 2024 AN: 5762

European-Non Finnish (NFE) AF: 0.328 AC: 363909 AN: 1110928

Other (OTH) AF: 0.325 AC: 19597 AN: 60336

GnomAD4 genome AF: 0.331 AC: 50282 AN: 151712 Hom.: 8404 Cov.: 0 AF XY: 0.335 AC XY: 24823 AN XY: 74126

African (AFR) AF: 0.323 AC: 13348 AN: 41360

American (AMR) AF: 0.283 AC: 4309 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1014 AN: 3466

East Asian (EAS) AF: 0.274 AC: 1408 AN: 5142

South Asian (SAS) AF: 0.430 AC: 2067 AN: 4806

European-Finnish (FIN) AF: 0.418 AC: 4397 AN: 10516

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22661 AN: 67864

Other (OTH) AF: 0.296 AC: 625 AN: 2110

Alfa AF: 0.330 Hom.: 1522

Bravo AF: 0.316

Asia WGS AF: 0.322 AC: 1127 AN: 3478

EpiCase AF: 0.326

EpiControl AF: 0.324

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.4
Mutation Taster		=82/18	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: rs139292; hg19: chr22-39496322; COSMIC: COSV62378588;