rs3730069
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015270.5(ADCY6):c.1833-29A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 1,612,492 control chromosomes in the GnomAD database, including 18,582 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.21 ( 5281 hom., cov: 32)
Exomes 𝑓: 0.12 ( 13301 hom. )
Consequence
ADCY6
NM_015270.5 intron
NM_015270.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.274
Genes affected
ADCY6 (HGNC:237): (adenylate cyclase 6) This gene encodes a member of the adenylyl cyclase family of proteins, which are required for the synthesis of cyclic AMP. All members of this family have an intracellular N-terminus, a tandem repeat of six transmembrane domains separated by a cytoplasmic loop, and a C-terminal cytoplasmic domain. The two cytoplasmic regions bind ATP and form the catalytic core of the protein. Adenylyl cyclases are important effectors of transmembrane signaling pathways and are regulated by the activity of G protein coupled receptor signaling. This protein belongs to a small subclass of adenylyl cyclase proteins that are functionally related and are inhibited by protein kinase A, calcium ions and nitric oxide. A mutation in this gene is associated with arthrogryposis multiplex congenita. [provided by RefSeq, May 2015]
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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=-0.79).
BP6
?
Variant 12-48775479-T-A is Benign according to our data. Variant chr12-48775479-T-A is described in ClinVar as [Benign]. Clinvar id is 1252860.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCY6 | NM_015270.5 | c.1833-29A>T | intron_variant | ENST00000357869.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCY6 | ENST00000357869.8 | c.1833-29A>T | intron_variant | 2 | NM_015270.5 | P1 | |||
ADCY6 | ENST00000307885.4 | c.1833-29A>T | intron_variant | 1 | P1 | ||||
ADCY6 | ENST00000550422.5 | c.1833-29A>T | intron_variant | 2 | |||||
ADCY6 | ENST00000552090.1 | n.355-29A>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.206 AC: 31349AN: 151844Hom.: 5269 Cov.: 32
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GnomAD3 exomes AF: 0.116 AC: 28928AN: 250308Hom.: 3013 AF XY: 0.110 AC XY: 14810AN XY: 135204
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GnomAD4 exome AF: 0.120 AC: 175611AN: 1460530Hom.: 13301 Cov.: 33 AF XY: 0.118 AC XY: 85863AN XY: 726456
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GnomAD4 genome ? AF: 0.207 AC: 31391AN: 151962Hom.: 5281 Cov.: 32 AF XY: 0.199 AC XY: 14794AN XY: 74282
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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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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at