rs7641344
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_183357.3(ADCY5):c.1134+31015C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0373 in 1,450,452 control chromosomes in the GnomAD database, including 6,352 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.082 ( 1194 hom., cov: 32)
Exomes 𝑓: 0.032 ( 5158 hom. )
Consequence
ADCY5
NM_183357.3 intron
NM_183357.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.810
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 3-123416397-G-A is Benign according to our data. Variant chr3-123416397-G-A is described in ClinVar as [Benign]. Clinvar id is 1260407.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADCY5 | NM_183357.3 | c.1134+31015C>T | intron_variant | ENST00000462833.6 | NP_899200.1 | |||
ADCY5 | NM_001378259.1 | c.1134+31015C>T | intron_variant | NP_001365188.1 | ||||
ADCY5 | XM_011512359.3 | c.135+8258C>T | intron_variant | XP_011510661.1 | ||||
ADCY5 | XM_047447359.1 | c.135+8258C>T | intron_variant | XP_047303315.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADCY5 | ENST00000462833.6 | c.1134+31015C>T | intron_variant | 1 | NM_183357.3 | ENSP00000419361.1 |
Frequencies
GnomAD3 genomes AF: 0.0819 AC: 12452AN: 152100Hom.: 1182 Cov.: 32
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GnomAD4 exome AF: 0.0321 AC: 41651AN: 1298234Hom.: 5158 AF XY: 0.0347 AC XY: 22012AN XY: 633810
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GnomAD4 genome AF: 0.0820 AC: 12480AN: 152218Hom.: 1194 Cov.: 32 AF XY: 0.0851 AC XY: 6335AN XY: 74420
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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 | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | - - |
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