rs2293004
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000488869(AADAC):c.-57C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,589,212 control chromosomes in the GnomAD database, including 80,337 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 0.31 ( 7490 hom., cov: 31)
Exomes 𝑓: 0.31 ( 72847 hom. )
Consequence
AADAC
ENST00000488869 5_prime_UTR
ENST00000488869 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.654
Genes affected
AADAC (HGNC:17): (arylacetamide deacetylase) Microsomal arylacetamide deacetylase competes against the activity of cytosolic arylamine N-acetyltransferase, which catalyzes one of the initial biotransformation pathways for arylamine and heterocyclic amine carcinogens [provided by RefSeq, Jul 2008]
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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=-0.88).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AADACL2-AS1 | NR_110202.1 | n.320-39441G>A | intron_variant | |||||
AADACL2-AS1 | NR_110203.1 | n.320-39441G>A | intron_variant | |||||
AADAC | NM_001086.3 | c.-57C>T | upstream_gene_variant | ENST00000232892.12 | NP_001077.2 | |||
AADAC | XM_005247104.5 | c.-57C>T | upstream_gene_variant | XP_005247161.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AADAC | ENST00000488869 | c.-57C>T | 5_prime_UTR_variant | 1/4 | 2 | ENSP00000419620.1 | ||||
AADACL2-AS1 | ENST00000475855.1 | n.320-39441G>A | intron_variant | 5 | ||||||
AADACL2-AS1 | ENST00000483843.6 | n.440-39441G>A | intron_variant | 5 | ||||||
AADAC | ENST00000232892.12 | c.-57C>T | upstream_gene_variant | 1 | NM_001086.3 | ENSP00000232892.6 |
Frequencies
GnomAD3 genomes AF: 0.305 AC: 46281AN: 151540Hom.: 7482 Cov.: 31
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GnomAD4 exome AF: 0.312 AC: 447979AN: 1437554Hom.: 72847 Cov.: 27 AF XY: 0.310 AC XY: 222439AN XY: 716612
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GnomAD4 genome AF: 0.305 AC: 46314AN: 151658Hom.: 7490 Cov.: 31 AF XY: 0.299 AC XY: 22154AN XY: 74062
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ClinVar
Not reported inComputational scores
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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