Variant rs61760501 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The ENST00000273857.9(CORIN):c.1188G>A(p.Thr396=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00307 in 1,614,052 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0020 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0032 ( 11 hom. )

Consequence

CORIN
ENST00000273857.9 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.83

Variant links:

Genes affected

CORIN (HGNC:19012): (corin, serine peptidase) This gene encodes a member of the type II transmembrane serine protease class of the trypsin superfamily. Members of this family are composed of multiple structurally distinct domains. The encoded protein converts pro-atrial natriuretic peptide to biologically active atrial natriuretic peptide, a cardiac hormone that regulates blood volume and pressure. This protein may also function as a pro-brain-type natriuretic peptide convertase. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2013]

CORIN links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 4-47677999-C-T is Benign according to our data. Variant chr4-47677999-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 778859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.83 with no splicing effect.

BS2

High AC in GnomAd4 at 310 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
CORIN	NM_006587.4 linkuse as main transcript	c.1188G>A	p.Thr396=	synonymous_variant	9/22	ENST00000273857.9	NP_006578.2
CORIN	NM_001278585.2 linkuse as main transcript	c.876G>A	p.Thr292=	synonymous_variant	7/20		NP_001265514.1
CORIN	NM_001278586.2 linkuse as main transcript	c.1077G>A	p.Thr359=	synonymous_variant	8/14		NP_001265515.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CORIN	ENST00000273857.9 linkuse as main transcript	c.1188G>A	p.Thr396=	synonymous_variant	9/22	1	NM_006587.4	ENSP00000273857	P2	Q9Y5Q5-1

Frequencies

GnomAD3 genomes

AF:

0.00204

AC:

310

AN:

152182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000796

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00177

Gnomad ASJ

AF:

0.000864

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00334

Gnomad OTH

AF:

0.00334

GnomAD3 exomes

AF:

0.00222

AC:

558

AN:

250888

Hom.:

AF XY:

0.00233

AC XY:

316

AN XY:

135574

show subpopulations

Gnomad AFR exome

AF:

0.000615

Gnomad AMR exome

AF:

0.00243

Gnomad ASJ exome

AF:

0.00139

Gnomad EAS exome

AF:

0.000872

Gnomad SAS exome

AF:

0.00163

Gnomad FIN exome

AF:

0.000416

Gnomad NFE exome

AF:

0.00312

Gnomad OTH exome

AF:

0.00359

GnomAD4 exome

AF:

0.00317

AC:

4639

AN:

1461752

Hom.:

Cov.:

AF XY:

0.00318

AC XY:

2315

AN XY:

727190

show subpopulations

Gnomad4 AFR exome

AF:

0.000358

Gnomad4 AMR exome

AF:

0.00264

Gnomad4 ASJ exome

AF:

0.00203

Gnomad4 EAS exome

AF:

0.000428

Gnomad4 SAS exome

AF:

0.00198

Gnomad4 FIN exome

AF:

0.000580

Gnomad4 NFE exome

AF:

0.00367

Gnomad4 OTH exome

AF:

0.00243

GnomAD4 genome

AF:

0.00204

AC:

310

AN:

152300

Hom.:

Cov.:

AF XY:

0.00167

AC XY:

124

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.000794

Gnomad4 AMR

AF:

0.00176

Gnomad4 ASJ

AF:

0.000864

Gnomad4 EAS

AF:

0.000772

Gnomad4 SAS

AF:

0.00146

Gnomad4 FIN

AF:

0.0000942

Gnomad4 NFE

AF:

0.00334

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00293

Hom.:

Bravo

AF:

0.00207

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.00360

EpiControl

AF:

0.00356

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jun 01, 2023	CORIN: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.17

DANN

Benign

0.56

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over