7-31076651-A-G

Variant names:

• chr7-31076651-A-G
• rs2267727
• NM_001118.5:c.158-1340A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001118.5(ADCYAP1R1):​c.158-1340A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,034 control chromosomes in the GnomAD database, including 1,220 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 (1220 hom., cov: 33)
• Consequence: ADCYAP1R1 NM_001118.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADCYAP1R1	NM_001118.5	c.158-1340A>G		intron_variant	Intron 3 of 15	ENST00000304166.9	NP_001109.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADCYAP1R1	ENST00000304166.9	c.158-1340A>G		intron_variant	Intron 3 of 15	2	NM_001118.5	ENSP00000306620.4

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17702 AN: 151916 Hom.: 1220 Cov.: 33

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.0937

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0750

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0547

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0919

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.117 AC: 17713 AN: 152034 Hom.: 1220 Cov.: 33 AF XY: 0.116 AC XY: 8592 AN XY: 74314

African (AFR) AF: 0.184 AC: 7608 AN: 41446

American (AMR) AF: 0.0935 AC: 1430 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 451 AN: 3470

East Asian (EAS) AF: 0.0748 AC: 385 AN: 5150

South Asian (SAS) AF: 0.131 AC: 630 AN: 4804

European-Finnish (FIN) AF: 0.0547 AC: 579 AN: 10580

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0919 AC: 6244 AN: 67972

Other (OTH) AF: 0.126 AC: 266 AN: 2112

Alfa AF: 0.101 Hom.: 1759

Bravo AF: 0.122

Asia WGS AF: 0.0920 AC: 320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.16
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2267727; hg19: chr7-31116266;