rs13317079
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_183357.3(ADCY5):c.*157G>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 0.00305 in 1,234,800 control chromosomes in the GnomAD database, including 79 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.014 ( 47 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 32 hom. )
Consequence
ADCY5
NM_183357.3 3_prime_UTR
NM_183357.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.420
Genes affected
ADCY5 (HGNC:236): (adenylate cyclase 5) This gene encodes a member of the membrane-bound adenylyl cyclase enzymes. Adenylyl cyclases mediate G protein-coupled receptor signaling through the synthesis of the second messenger cAMP. Activity of the encoded protein is stimulated by the Gs alpha subunit of G protein-coupled receptors and is inhibited by protein kinase A, calcium and Gi alpha subunits. Single nucleotide polymorphisms in this gene may be associated with low birth weight and type 2 diabetes. Alternatively spliced transcript variants that encode different isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]
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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=-0.41).
BP6
?
Variant 3-123284451-C-A is Benign according to our data. Variant chr3-123284451-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1197518.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0137 (2087/152370) while in subpopulation AFR AF= 0.0461 (1919/41588). AF 95% confidence interval is 0.0444. There are 47 homozygotes in gnomad4. There are 956 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 47 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCY5 | NM_183357.3 | c.*157G>T | 3_prime_UTR_variant | 21/21 | ENST00000462833.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCY5 | ENST00000462833.6 | c.*157G>T | 3_prime_UTR_variant | 21/21 | 1 | NM_183357.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0137 AC: 2088AN: 152252Hom.: 47 Cov.: 33
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GnomAD4 exome AF: 0.00155 AC: 1683AN: 1082430Hom.: 32 Cov.: 15 AF XY: 0.00138 AC XY: 740AN XY: 534320
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GnomAD4 genome ? AF: 0.0137 AC: 2087AN: 152370Hom.: 47 Cov.: 33 AF XY: 0.0128 AC XY: 956AN XY: 74510
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | - - |
Computational scores
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Name
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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