rs12628403
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_145699.4(APOBEC3A):c.470-66A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0935 in 1,555,134 control chromosomes in the GnomAD database, including 9,457 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 0.085 ( 942 hom., cov: 31)
Exomes 𝑓: 0.094 ( 8515 hom. )
Consequence
APOBEC3A
NM_145699.4 intron
NM_145699.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.122
Genes affected
APOBEC3A (HGNC:17343): (apolipoprotein B mRNA editing enzyme catalytic subunit 3A) 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 lacks the zinc binding activity of other family members. The protein plays a role in immunity, by restricting transmission of foreign DNA such as viruses. One mechanism of foreign DNA restriction is deamination of foreign double-stranded DNA cytidines to uridines, which leads to DNA degradation. However, other mechanisms are also thought to be involved, as anti-viral effect is not dependent on deaminase activity. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2012]
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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=-0.92).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOBEC3A | NM_145699.4 | c.470-66A>C | intron_variant | ENST00000249116.7 | |||
APOBEC3A | NM_001270406.2 | c.416-66A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOBEC3A | ENST00000249116.7 | c.470-66A>C | intron_variant | 1 | NM_145699.4 | P1 | |||
APOBEC3A | ENST00000402255.5 | c.470-66A>C | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0848 AC: 12876AN: 151874Hom.: 920 Cov.: 31
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GnomAD4 exome AF: 0.0944 AC: 132432AN: 1403142Hom.: 8515 AF XY: 0.0954 AC XY: 65883AN XY: 690844
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GnomAD4 genome ? AF: 0.0850 AC: 12919AN: 151992Hom.: 942 Cov.: 31 AF XY: 0.0899 AC XY: 6678AN XY: 74314
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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