rs17537588
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_021822.4(APOBEC3G):c.1141-88G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00911 in 1,604,596 control chromosomes in the GnomAD database, including 76 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 0.0071 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0093 ( 73 hom. )
Consequence
APOBEC3G
NM_021822.4 intron
NM_021822.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.69
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 -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.05).
BS2
?
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOBEC3G | NM_021822.4 | c.1141-88G>A | intron_variant | ENST00000407997.4 | |||
APOBEC3G | NM_001349436.1 | c.1108-88G>A | intron_variant | ||||
APOBEC3G | NM_001349437.2 | c.940-88G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOBEC3G | ENST00000407997.4 | c.1141-88G>A | intron_variant | 1 | NM_021822.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00709 AC: 1076AN: 151796Hom.: 3 Cov.: 32
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GnomAD4 exome AF: 0.00932 AC: 13540AN: 1452682Hom.: 73 Cov.: 31 AF XY: 0.00930 AC XY: 6724AN XY: 723386
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GnomAD4 genome ? AF: 0.00708 AC: 1076AN: 151914Hom.: 3 Cov.: 32 AF XY: 0.00668 AC XY: 496AN XY: 74246
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ClinVar
Not reported inComputational scores
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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