rs3736685
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021822.4(APOBEC3G):c.467-85T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0491 in 1,531,826 control chromosomes in the GnomAD database, including 6,158 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 0.13 ( 2992 hom., cov: 32)
Exomes 𝑓: 0.040 ( 3166 hom. )
Consequence
APOBEC3G
NM_021822.4 intron
NM_021822.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.19
Genes affected
APOBEC3G (HGNC:17357): (apolipoprotein B mRNA editing enzyme catalytic subunit 3G) This gene is a member of the cytidine deaminase gene family. It is one of seven related genes or pseudogenes 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. The protein encoded by this gene catalyzes site-specific deamination of both RNA and single-stranded DNA. The encoded protein has been found to be a specific inhibitor of human immunodeficiency virus-1 (HIV-1) infectivity. [provided by RefSeq, Mar 2017]
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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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOBEC3G | NM_021822.4 | c.467-85T>C | intron_variant | ENST00000407997.4 | NP_068594.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOBEC3G | ENST00000407997.4 | c.467-85T>C | intron_variant | 1 | NM_021822.4 | ENSP00000385057.3 |
Frequencies
GnomAD3 genomes AF: 0.130 AC: 19738AN: 152030Hom.: 2990 Cov.: 32
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GnomAD4 exome AF: 0.0401 AC: 55380AN: 1379678Hom.: 3166 Cov.: 23 AF XY: 0.0381 AC XY: 26238AN XY: 688462
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GnomAD4 genome AF: 0.130 AC: 19757AN: 152148Hom.: 2992 Cov.: 32 AF XY: 0.126 AC XY: 9395AN XY: 74390
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at