Variant rs8192597 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001099733.2(ADCYAP1):c.126G>A(p.Ala42Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 1,578,510 control chromosomes in the GnomAD database, including 405,027 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 0.67 ( 34761 hom., cov: 33)

Exomes 𝑓: 0.72 ( 370266 hom. )

Consequence

ADCYAP1
NM_001099733.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.809

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:

ADCYAP1 (HGNC:):

ADCYAP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP7

Synonymous conserved (PhyloP=-0.809 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADCYAP1	NM_001099733.2 linkuse as main transcript	c.126G>A	p.Ala42Ala	synonymous_variant	3/5	ENST00000450565.8	NP_001093203.1	P18509
ADCYAP1	NM_001117.5 linkuse as main transcript	c.126G>A	p.Ala42Ala	synonymous_variant	2/4		NP_001108.2	P18509
ADCYAP1	XM_005258081.5 linkuse as main transcript	c.543G>A	p.Ala181Ala	synonymous_variant	4/6		XP_005258138.2	B7Z222
ADCYAP1	XM_047437288.1 linkuse as main transcript	c.126G>A	p.Ala42Ala	synonymous_variant	3/5		XP_047293244.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ADCYAP1	ENST00000450565.8 linkuse as main transcript	c.126G>A	p.Ala42Ala	synonymous_variant	3/5	1	NM_001099733.2	ENSP00000411658.3	P18509
ADCYAP1	ENST00000579794.1 linkuse as main transcript	c.126G>A	p.Ala42Ala	synonymous_variant	2/4	1		ENSP00000462647.1	P18509
ADCYAP1	ENST00000269200.5 linkuse as main transcript	n.124G>A		non_coding_transcript_exon_variant	1/3	2
ENSG00000265671	ENST00000582554.1 linkuse as main transcript	n.7C>T		non_coding_transcript_exon_variant	1/2	5

Frequencies

GnomAD3 genomes

AF:

0.670

AC:

101879

AN:

151958

Hom.:

34741

Cov.:

show subpopulations

Gnomad AFR

AF:

0.533

Gnomad AMI

AF:

0.765

Gnomad AMR

AF:

0.757

Gnomad ASJ

AF:

0.610

Gnomad EAS

AF:

0.842

Gnomad SAS

AF:

0.759

Gnomad FIN

AF:

0.706

Gnomad MID

AF:

0.592

Gnomad NFE

AF:

0.713

Gnomad OTH

AF:

0.658

GnomAD3 exomes

AF:

0.729

AC:

146764

AN:

201196

Hom.:

53919

AF XY:

0.726

AC XY:

81080

AN XY:

111634

show subpopulations

Gnomad AFR exome

AF:

0.528

Gnomad AMR exome

AF:

0.818

Gnomad ASJ exome

AF:

0.607

Gnomad EAS exome

AF:

0.838

Gnomad SAS exome

AF:

0.757

Gnomad FIN exome

AF:

0.712

Gnomad NFE exome

AF:

0.711

Gnomad OTH exome

AF:

0.717

GnomAD4 exome

AF:

0.719

AC:

1025351

AN:

1426444

Hom.:

370266

Cov.:

AF XY:

0.719

AC XY:

509780

AN XY:

708882

show subpopulations

Gnomad4 AFR exome

AF:

0.522

Gnomad4 AMR exome

AF:

0.811

Gnomad4 ASJ exome

AF:

0.614

Gnomad4 EAS exome

AF:

0.856

Gnomad4 SAS exome

AF:

0.751

Gnomad4 FIN exome

AF:

0.714

Gnomad4 NFE exome

AF:

0.718

Gnomad4 OTH exome

AF:

0.701

GnomAD4 genome

AF:

0.670

AC:

101938

AN:

152066

Hom.:

34761

Cov.:

AF XY:

0.673

AC XY:

50025

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.532

Gnomad4 AMR

AF:

0.757

Gnomad4 ASJ

AF:

0.610

Gnomad4 EAS

AF:

0.842

Gnomad4 SAS

AF:

0.759

Gnomad4 FIN

AF:

0.706

Gnomad4 NFE

AF:

0.713

Gnomad4 OTH

AF:

0.659

Alfa

AF:

0.675

Hom.:

8165

Bravo

AF:

0.667

Asia WGS

AF:

0.764

AC:

2650

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

DANN

Benign

0.90

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over