rs2531995
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001116.4(ADCY9):c.*2309G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 395,602 control chromosomes in the GnomAD database, including 57,497 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 0.45 ( 18590 hom., cov: 31)
Exomes 𝑓: 0.55 ( 38907 hom. )
Consequence
ADCY9
NM_001116.4 3_prime_UTR
NM_001116.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0310
Genes affected
ADCY9 (HGNC:240): (adenylate cyclase 9) Adenylate cyclase is a membrane bound enzyme that catalyses the formation of cyclic AMP from ATP. It is regulated by a family of G protein-coupled receptors, protein kinases, and calcium. The type 9 adenylyl cyclase is a widely distributed adenylyl cyclase, and it is stimulated by beta-adrenergic receptor activation but is insensitive to forskolin, calcium, and somatostatin. [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=-0.79).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADCY9 | NM_001116.4 | c.*2309G>A | 3_prime_UTR_variant | 11/11 | ENST00000294016.8 | NP_001107.2 | ||
ADCY9 | XM_005255079.4 | c.*2309G>A | 3_prime_UTR_variant | 11/11 | XP_005255136.1 | |||
ADCY9 | XM_011522353.3 | c.2928-9950G>A | intron_variant | XP_011520655.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADCY9 | ENST00000294016.8 | c.*2309G>A | 3_prime_UTR_variant | 11/11 | 1 | NM_001116.4 | ENSP00000294016.3 | |||
ADCY9 | ENST00000576936.5 | c.567-9950G>A | intron_variant | 5 | ENSP00000460066.1 |
Frequencies
GnomAD3 genomes AF: 0.455 AC: 69111AN: 151876Hom.: 18599 Cov.: 31
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GnomAD4 exome AF: 0.553 AC: 134790AN: 243608Hom.: 38907 Cov.: 0 AF XY: 0.557 AC XY: 68878AN XY: 123616
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GnomAD4 genome AF: 0.455 AC: 69092AN: 151994Hom.: 18590 Cov.: 31 AF XY: 0.447 AC XY: 33221AN XY: 74298
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at