Genetic Variant ADCYAP1R1:c.1046+3122G>A (chr7-31095857-G-A) – 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.1046+3122G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 646,108 control chromosomes in the GnomAD database, including 88,905 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 0.56 ( 24363 hom., cov: 32)

Exomes 𝑓: 0.51 ( 64542 hom. )

Consequence

ADCYAP1R1
NM_001118.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

Publications

3 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:

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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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001118.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ADCYAP1R1	NM_001118.5	MANE Select	c.1046+3122G>A	intron	N/A	NP_001109.2
ADCYAP1R1	NM_001199635.2		c.1046+3122G>A	intron	N/A	NP_001186564.1
ADCYAP1R1	NM_001199636.2		c.1046+3122G>A	intron	N/A	NP_001186565.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ADCYAP1R1	ENST00000304166.9	TSL:2 MANE Select	c.1046+3122G>A	intron	N/A	ENSP00000306620.4
ADCYAP1R1	ENST00000396211.7	TSL:1	c.1046+3122G>A	intron	N/A	ENSP00000379514.2
ADCYAP1R1	ENST00000409363.5	TSL:1	c.983+3122G>A	intron	N/A	ENSP00000387335.1

Frequencies

GnomAD3 genomes

AF:

0.558

AC:

84649

AN:

151828

Hom.:

24334

Cov.:

show subpopulations

Gnomad AFR

AF:

0.692

Gnomad AMI

AF:

0.482

Gnomad AMR

AF:

0.454

Gnomad ASJ

AF:

0.489

Gnomad EAS

AF:

0.388

Gnomad SAS

AF:

0.456

Gnomad FIN

AF:

0.500

Gnomad MID

AF:

0.545

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.541

GnomAD4 exome

AF:

0.506

AC:

250068

AN:

494162

Hom.:

64542

AF XY:

0.504

AC XY:

132818

AN XY:

263632

show subpopulations

African (AFR)

AF:

0.688

AC:

9500

AN:

13800

American (AMR)

AF:

0.375

AC:

10216

AN:

27240

Ashkenazi Jewish (ASJ)

AF:

0.493

AC:

7801

AN:

15808

East Asian (EAS)

AF:

0.410

AC:

12876

AN:

31420

South Asian (SAS)

AF:

0.461

AC:

23780

AN:

51600

European-Finnish (FIN)

AF:

0.503

AC:

18260

AN:

36322

Middle Eastern (MID)

AF:

0.503

AC:

1179

AN:

2342

European-Non Finnish (NFE)

AF:

0.528

AC:

152098

AN:

287896

Other (OTH)

AF:

0.518

AC:

14358

AN:

27734

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

6345

12690

19036

25381

31726

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

710

1420

2130

2840

3550

<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:

0.558

AC:

84730

AN:

151946

Hom.:

24363

Cov.:

AF XY:

0.551

AC XY:

40923

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.692

AC:

28658

AN:

41432

American (AMR)

AF:

0.453

AC:

6923

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.489

AC:

1696

AN:

3470

East Asian (EAS)

AF:

0.388

AC:

1987

AN:

5122

South Asian (SAS)

AF:

0.457

AC:

2197

AN:

4804

European-Finnish (FIN)

AF:

0.500

AC:

5285

AN:

10578

Middle Eastern (MID)

AF:

0.555

AC:

162

AN:

292

European-Non Finnish (NFE)

AF:

0.533

AC:

36240

AN:

67944

Other (OTH)

AF:

0.541

AC:

1142

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1884

3768

5652

7536

9420

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

726

1452

2178

2904

3630

<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:

0.543

Hom.:

4623

Bravo

AF:

0.561

Asia WGS

AF:

0.444

AC:

1545

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.31

(source)

DANN

Benign

0.49

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over