chr1-167809606-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_018417.6(ADCY10):c.*72C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 1,538,322 control chromosomes in the GnomAD database, including 140,724 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.50 ( 20867 hom., cov: 32)
Exomes 𝑓: 0.41 ( 119857 hom. )
Consequence
ADCY10
NM_018417.6 3_prime_UTR
NM_018417.6 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0450
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=-0.86).
BP6
?
Variant 1-167809606-G-A is Benign according to our data. Variant chr1-167809606-G-A is described in ClinVar as [Benign]. Clinvar id is 1250999.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCY10 | NM_018417.6 | c.*72C>T | 3_prime_UTR_variant | 33/33 | ENST00000367851.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCY10 | ENST00000367851.9 | c.*72C>T | 3_prime_UTR_variant | 33/33 | 1 | NM_018417.6 | P1 | ||
ADCY10 | ENST00000545172.5 | c.*72C>T | 3_prime_UTR_variant | 30/30 | 2 | ||||
ADCY10 | ENST00000485964.5 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.496 AC: 75438AN: 151976Hom.: 20824 Cov.: 32
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GnomAD4 exome AF: 0.408 AC: 566029AN: 1386228Hom.: 119857 Cov.: 21 AF XY: 0.407 AC XY: 282317AN XY: 694168
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GnomAD4 genome ? AF: 0.497 AC: 75533AN: 152094Hom.: 20867 Cov.: 32 AF XY: 0.492 AC XY: 36555AN XY: 74348
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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
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at