rs10249706
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021116.4(ADCY1):c.*7757G>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 0.0719 in 398,504 control chromosomes in the GnomAD database, including 1,145 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 0.073 ( 456 hom., cov: 32)
Exomes 𝑓: 0.071 ( 689 hom. )
Consequence
ADCY1
NM_021116.4 3_prime_UTR
NM_021116.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.504
Genes affected
ADCY1 (HGNC:232): (adenylate cyclase 1) This gene encodes a member of the of adenylate cyclase gene family that is primarily expressed in the brain. This protein is regulated by calcium/calmodulin concentration and may be involved in brain development. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
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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=-0.67).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0735 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCY1 | NM_021116.4 | c.*7757G>A | 3_prime_UTR_variant | 20/20 | ENST00000297323.12 | ||
ADCY1 | XM_005249584.4 | c.*8052G>A | 3_prime_UTR_variant | 19/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCY1 | ENST00000297323.12 | c.*7757G>A | 3_prime_UTR_variant | 20/20 | 1 | NM_021116.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0731 AC: 11111AN: 152034Hom.: 456 Cov.: 32
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GnomAD4 exome AF: 0.0712 AC: 17536AN: 246352Hom.: 689 Cov.: 0 AF XY: 0.0718 AC XY: 8965AN XY: 124832
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GnomAD4 genome ? AF: 0.0731 AC: 11120AN: 152152Hom.: 456 Cov.: 32 AF XY: 0.0738 AC XY: 5490AN XY: 74378
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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