rs3884935

chr22-39024088-A-Gchr22-39024088-A-T

Variant summary

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

The NM_152426.4(APOBEC3D):c.211-982A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,192 control chromosomes in the GnomAD database, including 8,038 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 0.31 (8038 hom., cov: 32)
• Consequence: APOBEC3D NM_152426.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

Genes affected

APOBEC3D (HGNC:17354): (apolipoprotein B mRNA editing enzyme catalytic subunit 3D) This gene is a member of the cytidine deaminase gene family. It is one of a group of related genes found in a cluster, thought to result from gene duplication, on chromosome 22. Members of the cluster encode proteins that are structurally and functionally related to the C to U RNA-editing cytidine deaminase APOBEC1 and inhibit retroviruses, such as HIV, by deaminating cytosine residues in nascent retroviral cDNA. [provided by RefSeq, Jul 2008]

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 (AMR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOBEC3D	NM_152426.4	c.211-982A>G		intron_variant		ENST00000216099.13
APOBEC3D	NM_001363781.1	c.210+1074A>G		intron_variant
APOBEC3D	XM_017028596.3	c.211-982A>G		intron_variant
APOBEC3D	XM_047441142.1	c.211-982A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOBEC3D	ENST00000216099.13	c.211-982A>G		intron_variant		2	NM_152426.4	P1
APOBEC3D	ENST00000427494.6	c.210+1074A>G		intron_variant		1
APOBEC3D	ENST00000622217.3	c.17+2552A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47331 AN: 152072 Hom.: 8041 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.311 AC: 47335 AN: 152192 Hom.: 8038 Cov.: 32 AF XY: 0.308 AC XY: 22891 AN XY: 74406

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.361

Alfa AF: 0.175 Hom.: 352

Bravo AF: 0.321

Asia WGS AF: 0.312 AC: 1085 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	1.5
Dann	Benign	0.31

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: rs3884935; hg19: chr22-39420093;