chr7-31100932-G-A

Variant names:

• chr7-31100932-G-A
• rs2267742
• NM_001118.5:c.1047-2305G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ADCYAP1R1	NM_001118.5	c.1047-2305G>A		intron_variant	Intron 13 of 15	ENST00000304166.9	NP_001109.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADCYAP1R1	ENST00000304166.9	c.1047-2305G>A		intron_variant	Intron 13 of 15	2	NM_001118.5	ENSP00000306620.4

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

African (AFR) AF: 0.597 AC: 24723 AN: 41442

American (AMR) AF: 0.143 AC: 2180 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 529 AN: 3468

East Asian (EAS) AF: 0.187 AC: 967 AN: 5172

South Asian (SAS) AF: 0.193 AC: 933 AN: 4828

European-Finnish (FIN) AF: 0.0369 AC: 392 AN: 10622

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.0684 AC: 4648 AN: 67998

Other (OTH) AF: 0.210 AC: 444 AN: 2110

Alfa AF: 0.141 Hom.: 6792

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
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2267742; hg19: chr7-31140546;