rs203826
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_018417.6(ADCY10):c.1407-129G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 924,788 control chromosomes in the GnomAD database, including 41,308 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.34 ( 9820 hom., cov: 32)
Exomes 𝑓: 0.28 ( 31488 hom. )
Consequence
ADCY10
NM_018417.6 intron
NM_018417.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0910
Genes affected
ADCY10 (HGNC:21285): (adenylate cyclase 10) The protein encoded by this gene belongs to a distinct class of adenylyl cyclases that is soluble and insensitive to G protein or forskolin regulation. Activity of this protein is regulated by bicarbonate. Variation at this gene has been observed in patients with absorptive hypercalciuria. Alternatively spliced transcript variants encoding different isoforms have been observed. There is a pseudogene of this gene on chromosome 6. [provided by RefSeq, Jul 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 1-167875315-C-A is Benign according to our data. Variant chr1-167875315-C-A is described in ClinVar as [Benign]. Clinvar id is 1244897.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCY10 | NM_018417.6 | c.1407-129G>T | intron_variant | ENST00000367851.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCY10 | ENST00000367851.9 | c.1407-129G>T | intron_variant | 1 | NM_018417.6 | P1 | |||
ADCY10 | ENST00000367848.1 | c.1131-129G>T | intron_variant | 1 | |||||
ADCY10 | ENST00000545172.5 | c.948-129G>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.340 AC: 51722AN: 151966Hom.: 9811 Cov.: 32
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GnomAD4 exome AF: 0.278 AC: 214558AN: 772704Hom.: 31488 AF XY: 0.272 AC XY: 110306AN XY: 404822
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GnomAD4 genome ? AF: 0.340 AC: 51774AN: 152084Hom.: 9820 Cov.: 32 AF XY: 0.338 AC XY: 25107AN XY: 74362
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at