rs2267742

Positions:

• chr7-31100932-G-A
• chr7-31100932-G-C
• chr7-31100932-G-T

Variant summary

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

The NM_001118.5(ADCYAP1R1):​c.1047-2305G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,140 control chromosomes in the GnomAD database, including 8,066 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 0.23 (8066 hom., cov: 33)
• Consequence: ADCYAP1R1 NM_001118.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.251

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADCYAP1R1	NM_001118.5	c.1047-2305G>A		intron_variant		ENST00000304166.9	NP_001109.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADCYAP1R1	ENST00000304166.9	c.1047-2305G>A		intron_variant		2	NM_001118.5	ENSP00000306620	A1

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34833 AN: 152022 Hom.: 8038 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.0369

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.0683

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.229 AC: 34913 AN: 152140 Hom.: 8066 Cov.: 33 AF XY: 0.226 AC XY: 16812 AN XY: 74404

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.0369

Gnomad4 NFE AF: 0.0684

Gnomad4 OTH AF: 0.210

Alfa AF: 0.143 Hom.: 1075

Bravo AF: 0.252

Asia WGS AF: 0.255 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.1
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2267742; hg19: chr7-31140546;