dbSNP rs2302475: ADCYAP1R1:c.328+132T>C (chr7-31081886-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001118.5(ADCYAP1R1):c.328+132T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 637,786 control chromosomes in the GnomAD database, including 70,194 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 0.48 ( 17364 hom., cov: 32)

Exomes 𝑓: 0.46 ( 52830 hom. )

Consequence

ADCYAP1R1
NM_001118.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.466

Publications

4 publications found

Variant links:

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]

ADCYAP1R1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADCYAP1R1	NM_001118.5 link	c.328+132T>C		intron_variant	Intron 6 of 15	ENST00000304166.9	NP_001109.2	P41586-1A0A090N8F8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADCYAP1R1	ENST00000304166.9 link	c.328+132T>C		intron_variant	Intron 6 of 15	2	NM_001118.5	ENSP00000306620.4		P41586-1

Frequencies

GnomAD3 genomes

AF:

0.476

AC:

72198

AN:

151806

Hom.:

17349

Cov.:

show subpopulations

Gnomad AFR

AF:

0.512

Gnomad AMI

AF:

0.455

Gnomad AMR

AF:

0.435

Gnomad ASJ

AF:

0.381

Gnomad EAS

AF:

0.522

Gnomad SAS

AF:

0.390

Gnomad FIN

AF:

0.527

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.463

Gnomad OTH

AF:

0.451

GnomAD4 exome

AF:

0.465

AC:

225804

AN:

485860

Hom.:

52830

AF XY:

0.462

AC XY:

116866

AN XY:

252850

show subpopulations

African (AFR)

AF:

0.508

AC:

6282

AN:

12354

American (AMR)

AF:

0.448

AC:

8268

AN:

18468

Ashkenazi Jewish (ASJ)

AF:

0.375

AC:

4934

AN:

13154

East Asian (EAS)

AF:

0.517

AC:

15220

AN:

29436

South Asian (SAS)

AF:

0.397

AC:

12032

AN:

30270

European-Finnish (FIN)

AF:

0.524

AC:

23584

AN:

44982

Middle Eastern (MID)

AF:

0.388

AC:

788

AN:

2032

European-Non Finnish (NFE)

AF:

0.461

AC:

142542

AN:

309026

Other (OTH)

AF:

0.465

AC:

12154

AN:

26138

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

5805

11610

17416

23221

29026

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1856

3712

5568

7424

9280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.475

AC:

72240

AN:

151926

Hom.:

17364

Cov.:

AF XY:

0.477

AC XY:

35438

AN XY:

74252

show subpopulations

African (AFR)

AF:

0.512

AC:

21162

AN:

41360

American (AMR)

AF:

0.436

AC:

6658

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.381

AC:

1322

AN:

3468

East Asian (EAS)

AF:

0.522

AC:

2696

AN:

5162

South Asian (SAS)

AF:

0.389

AC:

1874

AN:

4820

European-Finnish (FIN)

AF:

0.527

AC:

5572

AN:

10570

Middle Eastern (MID)

AF:

0.391

AC:

115

AN:

294

European-Non Finnish (NFE)

AF:

0.463

AC:

31480

AN:

67956

Other (OTH)

AF:

0.448

AC:

946

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1942

3884

5825

7767

9709

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

662

1324

1986

2648

3310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.467

Hom.:

54387

Bravo

AF:

0.478

Asia WGS

AF:

0.432

AC:

1504

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.7

(source)

DANN

Benign

0.78

PhyloP100

0.47

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over