rs10081254

Positions:

• chr7-31082056-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001118.5(ADCYAP1R1):​c.328+302C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,206 control chromosomes in the GnomAD database, including 1,486 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 0.12 (1486 hom., cov: 33)
• Consequence: ADCYAP1R1 NM_001118.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADCYAP1R1	NM_001118.5	c.328+302C>T		intron_variant		ENST00000304166.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADCYAP1R1	ENST00000304166.9	c.328+302C>T		intron_variant		2	NM_001118.5	A1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18104 AN: 152088 Hom.: 1483 Cov.: 33

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0835

Gnomad EAS AF: 0.0620

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0291

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.120

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.119 AC: 18144 AN: 152206 Hom.: 1486 Cov.: 33 AF XY: 0.116 AC XY: 8610 AN XY: 74420

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0835

Gnomad4 EAS AF: 0.0618

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0291

Gnomad4 NFE AF: 0.0765

Gnomad4 OTH AF: 0.122

Alfa AF: 0.102 Hom.: 287

Bravo AF: 0.129

Asia WGS AF: 0.102 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.26
DANN	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10081254; hg19: chr7-31121671;