22-39099665-C-T

Position:

• chr22-39099665-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.-7-607C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 152,076 control chromosomes in the GnomAD database, including 13,686 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 0.42 (13686 hom., cov: 32)
• Consequence: APOBEC3H NM_181773.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.686

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]

APOBEC3H (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOBEC3H	NM_181773.5	c.-7-607C>T		intron_variant		ENST00000442487.8	NP_861438.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOBEC3H	ENST00000442487.8	c.-7-607C>T		intron_variant		3	NM_181773.5	ENSP00000411754.3

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63064 AN: 151956 Hom.: 13652 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.360

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.415 AC: 63156 AN: 152076 Hom.: 13686 Cov.: 32 AF XY: 0.418 AC XY: 31089 AN XY: 74358

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.356

Alfa AF: 0.381 Hom.: 2131

Bravo AF: 0.406

Asia WGS AF: 0.378 AC: 1323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.41

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: rs139284; hg19: chr22-39495670;