rs5750743
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001349436.1(APOBEC3G):c.-144C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000504 in 138,758 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000050 ( 0 hom., cov: 28)
Exomes 𝑓: 0.000074 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
APOBEC3G
NM_001349436.1 5_prime_UTR
NM_001349436.1 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0400
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 Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOBEC3G | NM_001349436.1 | c.-144C>A | 5_prime_UTR_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOBEC3G | ENST00000461827.5 | upstream_gene_variant | 3 | ||||||
APOBEC3G | ENST00000463934.1 | upstream_gene_variant | 2 | ||||||
APOBEC3G | ENST00000480000.5 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000504 AC: 7AN: 138758Hom.: 0 Cov.: 28
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000744 AC: 25AN: 336116Hom.: 0 Cov.: 3 AF XY: 0.0000567 AC XY: 10AN XY: 176420
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GnomAD4 genome ? AF: 0.0000504 AC: 7AN: 138758Hom.: 0 Cov.: 28 AF XY: 0.0000443 AC XY: 3AN XY: 67738
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at