Variant rs2231187 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001099733.2(ADCYAP1):c.456A>G(p.Lys152=) variant causes a synonymous change. The variant allele was found at a frequency of 0.299 in 1,613,706 control chromosomes in the GnomAD database, including 75,260 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 ( 5604 hom., cov: 32)

Exomes 𝑓: 0.30 ( 69656 hom. )

Consequence

ADCYAP1
NM_001099733.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.16

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ADCYAP1	NM_001099733.2 linkuse as main transcript	c.456A>G	p.Lys152=	synonymous_variant	5/5	ENST00000450565.8
ADCYAP1	NM_001117.5 linkuse as main transcript	c.456A>G	p.Lys152=	synonymous_variant	4/4
ADCYAP1	XM_005258081.5 linkuse as main transcript	c.873A>G	p.Lys291=	synonymous_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
ADCYAP1	ENST00000450565.8 linkuse as main transcript	c.456A>G	p.Lys152=	synonymous_variant	5/5	1	NM_001099733.2	P1
ADCYAP1	ENST00000579794.1 linkuse as main transcript	c.456A>G	p.Lys152=	synonymous_variant	4/4	1		P1
ADCYAP1	ENST00000269200.5 linkuse as main transcript	n.454A>G		non_coding_transcript_exon_variant	3/3	2
ADCYAP1	ENST00000581602.1 linkuse as main transcript	n.447A>G		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38828

AN:

152056

Hom.:

5597

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.164

Gnomad AMR

AF:

0.300

Gnomad ASJ

AF:

0.244

Gnomad EAS

AF:

0.232

Gnomad SAS

AF:

0.163

Gnomad FIN

AF:

0.332

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.327

Gnomad OTH

AF:

0.263

GnomAD3 exomes

AF:

0.281

AC:

70556

AN:

251174

Hom.:

10691

AF XY:

0.276

AC XY:

37436

AN XY:

135816

show subpopulations

Gnomad AFR exome

AF:

0.112

Gnomad AMR exome

AF:

0.336

Gnomad ASJ exome

AF:

0.245

Gnomad EAS exome

AF:

0.232

Gnomad SAS exome

AF:

0.158

Gnomad FIN exome

AF:

0.339

Gnomad NFE exome

AF:

0.320

Gnomad OTH exome

AF:

0.292

GnomAD4 exome

AF:

0.303

AC:

442894

AN:

1461532

Hom.:

69656

Cov.:

AF XY:

0.298

AC XY:

216880

AN XY:

727058

show subpopulations

Gnomad4 AFR exome

AF:

0.106

Gnomad4 AMR exome

AF:

0.336

Gnomad4 ASJ exome

AF:

0.246

Gnomad4 EAS exome

AF:

0.229

Gnomad4 SAS exome

AF:

0.162

Gnomad4 FIN exome

AF:

0.338

Gnomad4 NFE exome

AF:

0.322

Gnomad4 OTH exome

AF:

0.287

GnomAD4 genome

AF:

0.255

AC:

38843

AN:

152174

Hom.:

5604

Cov.:

AF XY:

0.252

AC XY:

18716

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.118

Gnomad4 AMR

AF:

0.301

Gnomad4 ASJ

AF:

0.244

Gnomad4 EAS

AF:

0.232

Gnomad4 SAS

AF:

0.161

Gnomad4 FIN

AF:

0.332

Gnomad4 NFE

AF:

0.327

Gnomad4 OTH

AF:

0.264

Alfa

AF:

0.297

Hom.:

6894

Bravo

AF:

0.249

Asia WGS

AF:

0.169

AC:

590

AN:

3478

EpiCase

AF:

0.314

EpiControl

AF:

0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Benign

0.69

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