dbSNP rs1610037: ADCYAP1:c.*999A>G (chr18-910634-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001099733.2(ADCYAP1):c.*999A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,168 control chromosomes in the GnomAD database, including 5,806 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 0.26 ( 5801 hom., cov: 32)

Exomes 𝑓: 0.36 ( 5 hom. )

Consequence

ADCYAP1
NM_001099733.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00600

Publications

12 publications found

Variant links:

Genes affected

ADCYAP1 (HGNC:241): (adenylate cyclase activating polypeptide 1) This gene encodes a secreted proprotein that is further processed into multiple mature peptides. These peptides stimulate adenylate cyclase and increase cyclic adenosine monophosphate (cAMP) levels, resulting in the transcriptional activation of target genes. The products of this gene are key mediators of neuroendocrine stress responses. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2013]

ADCYAP1 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ADCYAP1	NM_001099733.2 link	c.*999A>G	3_prime_UTR_variant	Exon 5 of 5	ENST00000450565.8	NP_001093203.1	P18509
ADCYAP1	NM_001117.5 link	c.*999A>G	3_prime_UTR_variant	Exon 4 of 4		NP_001108.2	P18509
ADCYAP1	XM_005258081.5 link	c.*999A>G	3_prime_UTR_variant	Exon 6 of 6		XP_005258138.2	B7Z222

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ADCYAP1	ENST00000450565.8 link	c.*999A>G	3_prime_UTR_variant	Exon 5 of 5	1	NM_001099733.2	ENSP00000411658.3	P18509
ADCYAP1	ENST00000579794.1 link	c.*999A>G	3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000462647.1	P18509
ADCYAP1	ENST00000581602.1 link	n.1521A>G	non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

40010

AN:

152008

Hom.:

5805

Cov.:

show subpopulations

Gnomad AFR

AF:

0.142

Gnomad AMI

AF:

0.285

Gnomad AMR

AF:

0.276

Gnomad ASJ

AF:

0.478

Gnomad EAS

AF:

0.225

Gnomad SAS

AF:

0.303

Gnomad FIN

AF:

0.310

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.315

Gnomad OTH

AF:

0.271

GnomAD4 exome

AF:

0.357

AC:

AN:

Hom.:

Cov.:

AF XY:

0.294

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.265

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<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:

0.263

AC:

40007

AN:

152126

Hom.:

5801

Cov.:

AF XY:

0.265

AC XY:

19722

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.142

AC:

5905

AN:

41534

American (AMR)

AF:

0.275

AC:

4210

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.478

AC:

1660

AN:

3470

East Asian (EAS)

AF:

0.225

AC:

1162

AN:

5168

South Asian (SAS)

AF:

0.303

AC:

1462

AN:

4826

European-Finnish (FIN)

AF:

0.310

AC:

3274

AN:

10564

Middle Eastern (MID)

AF:

0.344

AC:

101

AN:

294

European-Non Finnish (NFE)

AF:

0.315

AC:

21410

AN:

67968

Other (OTH)

AF:

0.267

AC:

564

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1467

2934

4400

5867

7334

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

424

848

1272

1696

2120

<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:

0.303

Hom.:

14072

Bravo

AF:

0.252

Asia WGS

AF:

0.242

AC:

845

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

3.1

(source)

DANN

Benign

0.50

PhyloP100

0.0060

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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