rs3884935
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
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
NM_152426.4 intron
Scores
2
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]
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ACMG classification
Classification made for transcript
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOBEC3D | NM_152426.4 | c.211-982A>G | intron_variant | ENST00000216099.13 | NP_689639.2 | |||
APOBEC3D | NM_001363781.1 | c.210+1074A>G | intron_variant | NP_001350710.1 | ||||
APOBEC3D | XM_017028596.3 | c.211-982A>G | intron_variant | XP_016884085.1 | ||||
APOBEC3D | XM_047441142.1 | c.211-982A>G | intron_variant | XP_047297098.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOBEC3D | ENST00000216099.13 | c.211-982A>G | intron_variant | 2 | NM_152426.4 | ENSP00000216099.7 | ||||
ENSG00000284554 | ENST00000381568.9 | c.211-982A>G | intron_variant | 1 | ENSP00000370980.4 | |||||
APOBEC3D | ENST00000427494.6 | c.210+1074A>G | intron_variant | 1 | ENSP00000388017.2 | |||||
APOBEC3D | ENST00000622217.3 | c.17+2552A>G | intron_variant | 5 | ENSP00000480718.3 |
Frequencies
GnomAD3 genomes AF: 0.311 AC: 47331AN: 152072Hom.: 8041 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.311 AC: 47335AN: 152192Hom.: 8038 Cov.: 32 AF XY: 0.308 AC XY: 22891AN XY: 74406
GnomAD4 genome
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1085
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at