rs139316
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_181773.5(APOBEC3H):c.*61T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 1,595,670 control chromosomes in the GnomAD database, including 182,067 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 0.54 ( 23615 hom., cov: 31)
Exomes 𝑓: 0.46 ( 158452 hom. )
Consequence
APOBEC3H
NM_181773.5 3_prime_UTR
NM_181773.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0580
Genes affected
APOBEC3H (HGNC:24100): (apolipoprotein B mRNA editing enzyme catalytic subunit 3H) This gene encodes a member of the apolipoprotein B mRNA-editing enzyme catalytic polypeptide 3 family of proteins. The encoded protein is a cytidine deaminase that has antiretroviral activity by generating lethal hypermutations in viral genomes. Polymorphisms and alternative splicing in this gene influence its antiretroviral activity and are associated with increased resistence to human immunodeficiency virus type 1 infection in certain populations. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Oct 2009]
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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 (AFR) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOBEC3H | NM_181773.5 | c.*61T>C | 3_prime_UTR_variant | 5/5 | ENST00000442487.8 | NP_861438.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOBEC3H | ENST00000442487.8 | c.*61T>C | 3_prime_UTR_variant | 5/5 | 3 | NM_181773.5 | ENSP00000411754.3 | |||
APOBEC3H | ENST00000348946.8 | c.*61T>C | 3_prime_UTR_variant | 5/5 | 1 | ENSP00000216123.5 | ||||
APOBEC3H | ENST00000401756.5 | c.*104T>C | 3_prime_UTR_variant | 6/6 | 3 | ENSP00000385741.1 |
Frequencies
GnomAD3 genomes AF: 0.539 AC: 81924AN: 151896Hom.: 23587 Cov.: 31
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GnomAD4 exome AF: 0.463 AC: 668026AN: 1443656Hom.: 158452 Cov.: 31 AF XY: 0.463 AC XY: 333396AN XY: 719346
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GnomAD4 genome AF: 0.539 AC: 82006AN: 152014Hom.: 23615 Cov.: 31 AF XY: 0.537 AC XY: 39935AN XY: 74300
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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