chr1-167880176-A-G
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_018417.6(ADCY10):āc.1155T>Cā(p.Gly385=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 1,610,082 control chromosomes in the GnomAD database, including 187,779 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.52 ( 20842 hom., cov: 32)
Exomes š: 0.48 ( 166937 hom. )
Consequence
ADCY10
NM_018417.6 synonymous
NM_018417.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.909
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 -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 1-167880176-A-G is Benign according to our data. Variant chr1-167880176-A-G is described in ClinVar as [Benign]. Clinvar id is 1167837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.909 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCY10 | NM_018417.6 | c.1155T>C | p.Gly385= | synonymous_variant | 11/33 | ENST00000367851.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCY10 | ENST00000367851.9 | c.1155T>C | p.Gly385= | synonymous_variant | 11/33 | 1 | NM_018417.6 | P1 | |
ADCY10 | ENST00000367848.1 | c.879T>C | p.Gly293= | synonymous_variant | 11/33 | 1 | |||
ADCY10 | ENST00000545172.5 | c.696T>C | p.Gly232= | synonymous_variant | 8/30 | 2 |
Frequencies
GnomAD3 genomes AF: 0.516 AC: 78436AN: 151936Hom.: 20819 Cov.: 32
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GnomAD3 exomes AF: 0.473 AC: 117391AN: 247990Hom.: 28231 AF XY: 0.472 AC XY: 63202AN XY: 133826
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GnomAD4 exome AF: 0.476 AC: 694420AN: 1458028Hom.: 166937 Cov.: 38 AF XY: 0.476 AC XY: 345478AN XY: 725160
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GnomAD4 genome AF: 0.516 AC: 78507AN: 152054Hom.: 20842 Cov.: 32 AF XY: 0.514 AC XY: 38213AN XY: 74342
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at