rs2601828
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001116.4(ADCY9):c.1694-46312A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 151,960 control chromosomes in the GnomAD database, including 45,029 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 0.77 ( 45029 hom., cov: 29)
Consequence
ADCY9
NM_001116.4 intron
NM_001116.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.750
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=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCY9 | NM_001116.4 | c.1694-46312A>G | intron_variant | ENST00000294016.8 | |||
LOC124900373 | XR_007064957.1 | n.587-49A>G | intron_variant, non_coding_transcript_variant | ||||
ADCY9 | XM_005255079.4 | c.1694-46312A>G | intron_variant | ||||
ADCY9 | XM_011522353.3 | c.1694-46312A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCY9 | ENST00000294016.8 | c.1694-46312A>G | intron_variant | 1 | NM_001116.4 | P1 | |||
ADCY9 | ENST00000572288.1 | c.278-46312A>G | intron_variant | 4 | |||||
ADCY9 | ENST00000571467.1 | c.176+59880A>G | intron_variant, NMD_transcript_variant | 5 | |||||
ADCY9 | ENST00000571889.1 | n.156+165A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.767 AC: 116452AN: 151842Hom.: 44983 Cov.: 29
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.767 AC: 116543AN: 151960Hom.: 45029 Cov.: 29 AF XY: 0.765 AC XY: 56791AN XY: 74246
GnomAD4 genome
?
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116543
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151960
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56791
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74246
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2559
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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