Variant chr7-31078019-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001118.5(ADCYAP1R1):c.186G>A(p.Thr62=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00278 in 1,612,722 control chromosomes in the GnomAD database, including 51 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0053 ( 12 hom., cov: 33)

Exomes 𝑓: 0.0025 ( 39 hom. )

Consequence

ADCYAP1R1
NM_001118.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -5.25

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 made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 7-31078019-G-A is Benign according to our data. Variant chr7-31078019-G-A is described in ClinVar as [Benign]. Clinvar id is 768144.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-5.25 with no splicing effect.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00532 (810/152184) while in subpopulation EAS AF= 0.021 (109/5188). AF 95% confidence interval is 0.0178. There are 12 homozygotes in gnomad4. There are 498 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 12 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADCYAP1R1	NM_001118.5 linkuse as main transcript	c.186G>A	p.Thr62=	synonymous_variant	4/16	ENST00000304166.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADCYAP1R1	ENST00000304166.9 linkuse as main transcript	c.186G>A	p.Thr62=	synonymous_variant	4/16	2	NM_001118.5	A1	P41586-1

Frequencies

GnomAD3 genomes

AF:

0.00532

AC:

809

AN:

152066

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00652

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00177

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.0213

Gnomad SAS

AF:

0.00870

Gnomad FIN

AF:

0.0239

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00140

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00568

AC:

1420

AN:

250052

Hom.:

AF XY:

0.00594

AC XY:

802

AN XY:

135106

show subpopulations

Gnomad AFR exome

AF:

0.00560

Gnomad AMR exome

AF:

0.00136

Gnomad ASJ exome

AF:

0.00111

Gnomad EAS exome

AF:

0.0220

Gnomad SAS exome

AF:

0.00641

Gnomad FIN exome

AF:

0.0215

Gnomad NFE exome

AF:

0.00156

Gnomad OTH exome

AF:

0.00492

GnomAD4 exome

AF:

0.00251

AC:

3667

AN:

1460538

Hom.:

Cov.:

AF XY:

0.00272

AC XY:

1976

AN XY:

726556

show subpopulations

Gnomad4 AFR exome

AF:

0.00628

Gnomad4 AMR exome

AF:

0.00157

Gnomad4 ASJ exome

AF:

0.00119

Gnomad4 EAS exome

AF:

0.0140

Gnomad4 SAS exome

AF:

0.00658

Gnomad4 FIN exome

AF:

0.0200

Gnomad4 NFE exome

AF:

0.000756

Gnomad4 OTH exome

AF:

0.00396

GnomAD4 genome

AF:

0.00532

AC:

810

AN:

152184

Hom.:

Cov.:

AF XY:

0.00669

AC XY:

498

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.00658

Gnomad4 AMR

AF:

0.00177

Gnomad4 ASJ

AF:

0.000577

Gnomad4 EAS

AF:

0.0210

Gnomad4 SAS

AF:

0.00871

Gnomad4 FIN

AF:

0.0239

Gnomad4 NFE

AF:

0.00140

Gnomad4 OTH

AF:

0.00332

Alfa

AF:

0.00186

Hom.:

Bravo

AF:

0.00362

Asia WGS

AF:

0.0140

AC:

AN:

3478

EpiCase

AF:

0.00224

EpiControl

AF:

0.00202

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Aug 21, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.44

DANN

Benign

0.78

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over