rs1893154
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000579794.1(ADCYAP1):c.-263A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 1,364,876 control chromosomes in the GnomAD database, including 385,695 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 0.72 ( 39710 hom., cov: 33)
Exomes 𝑓: 0.75 ( 345985 hom. )
Consequence
ADCYAP1
ENST00000579794.1 5_prime_UTR
ENST00000579794.1 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.239
Genes affected
ADCYAP1 (HGNC:241): (adenylate cyclase activating polypeptide 1) This gene encodes a secreted proprotein that is further processed into multiple mature peptides. These peptides stimulate adenylate cyclase and increase cyclic adenosine monophosphate (cAMP) levels, resulting in the transcriptional activation of target genes. The products of this gene are key mediators of neuroendocrine stress responses. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2013]
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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=-0.85).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADCYAP1 | NM_001099733.2 | c.-2+64A>G | intron_variant | ENST00000450565.8 | |||
LOC124904340 | XR_007066435.1 | n.1529T>C | non_coding_transcript_exon_variant | 1/2 | |||
ADCYAP1 | XM_005258081.5 | c.416+64A>G | intron_variant | ||||
ADCYAP1 | XM_047437288.1 | c.-2+64A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADCYAP1 | ENST00000450565.8 | c.-2+64A>G | intron_variant | 1 | NM_001099733.2 | P1 | |||
ENST00000581719.3 | n.1544T>C | non_coding_transcript_exon_variant | 1/1 | ||||||
ENST00000582554.1 | n.90+2467T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.719 AC: 109252AN: 151988Hom.: 39683 Cov.: 33
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GnomAD4 exome AF: 0.754 AC: 913975AN: 1212774Hom.: 345985 Cov.: 56 AF XY: 0.752 AC XY: 440582AN XY: 585656
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GnomAD4 genome ? AF: 0.719 AC: 109324AN: 152102Hom.: 39710 Cov.: 33 AF XY: 0.720 AC XY: 53531AN XY: 74386
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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