rs758995
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001118.5(ADCYAP1R1):c.157+12G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 1,590,046 control chromosomes in the GnomAD database, including 13,917 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.16 ( 2751 hom., cov: 33)
Exomes 𝑓: 0.12 ( 11166 hom. )
Consequence
ADCYAP1R1
NM_001118.5 intron
NM_001118.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.465
Genes affected
ADCYAP1R1 (HGNC:242): (ADCYAP receptor type I) This gene encodes type I adenylate cyclase activating polypeptide receptor, which is a membrane-associated protein and shares significant homology with members of the glucagon/secretin receptor family. This receptor mediates diverse biological actions of adenylate cyclase activating polypeptide 1 and is positively coupled to adenylate cyclase. Multiple alternatively spliced transcript variants encoding distinct isoforms have been identified. [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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCYAP1R1 | NM_001118.5 | c.157+12G>A | intron_variant | ENST00000304166.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCYAP1R1 | ENST00000304166.9 | c.157+12G>A | intron_variant | 2 | NM_001118.5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.165 AC: 25042AN: 152080Hom.: 2736 Cov.: 33
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GnomAD3 exomes AF: 0.116 AC: 25413AN: 219266Hom.: 1920 AF XY: 0.115 AC XY: 13462AN XY: 117508
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GnomAD4 exome AF: 0.118 AC: 170221AN: 1437848Hom.: 11166 Cov.: 28 AF XY: 0.118 AC XY: 84314AN XY: 713570
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GnomAD4 genome ? AF: 0.165 AC: 25095AN: 152198Hom.: 2751 Cov.: 33 AF XY: 0.160 AC XY: 11917AN XY: 74424
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ClinVar
Not reported inComputational 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