Variant rs61759670 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_006587.4(CORIN):c.2721C>T(p.Tyr907Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0208 in 1,614,098 control chromosomes in the GnomAD database, including 729 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 0.018 ( 54 hom., cov: 32)

Exomes 𝑓: 0.021 ( 675 hom. )

Consequence

CORIN
NM_006587.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.229

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP7

Synonymous conserved (PhyloP=-0.229 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CORIN	NM_006587.4 linkuse as main transcript	c.2721C>T	p.Tyr907Tyr	synonymous_variant	20/22	ENST00000273857.9	NP_006578.2	Q9Y5Q5-1B4E2W9
CORIN	NM_001278585.2 linkuse as main transcript	c.2409C>T	p.Tyr803Tyr	synonymous_variant	18/20		NP_001265514.1	Q9Y5Q5A0A087X1D5B4E1Y7B4E2W9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CORIN	ENST00000273857.9 linkuse as main transcript	c.2721C>T	p.Tyr907Tyr	synonymous_variant	20/22	1	NM_006587.4	ENSP00000273857.4		Q9Y5Q5-1

Frequencies

GnomAD3 genomes

AF:

0.0178

AC:

2705

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00314

Gnomad AMI

AF:

0.0186

Gnomad AMR

AF:

0.0267

Gnomad ASJ

AF:

0.0613

Gnomad EAS

AF:

0.000963

Gnomad SAS

AF:

0.0774

Gnomad FIN

AF:

0.00839

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0203

Gnomad OTH

AF:

0.0292

GnomAD3 exomes

AF:

0.0271

AC:

6803

AN:

250982

Hom.:

202

AF XY:

0.0311

AC XY:

4215

AN XY:

135698

show subpopulations

Gnomad AFR exome

AF:

0.00296

Gnomad AMR exome

AF:

0.0190

Gnomad ASJ exome

AF:

0.0555

Gnomad EAS exome

AF:

0.000272

Gnomad SAS exome

AF:

0.0866

Gnomad FIN exome

AF:

0.0103

Gnomad NFE exome

AF:

0.0218

Gnomad OTH exome

AF:

0.0307

GnomAD4 exome

AF:

0.0212

AC:

30940

AN:

1461824

Hom.:

675

Cov.:

AF XY:

0.0235

AC XY:

17085

AN XY:

727210

show subpopulations

Gnomad4 AFR exome

AF:

0.00344

Gnomad4 AMR exome

AF:

0.0190

Gnomad4 ASJ exome

AF:

0.0541

Gnomad4 EAS exome

AF:

0.000252

Gnomad4 SAS exome

AF:

0.0825

Gnomad4 FIN exome

AF:

0.0108

Gnomad4 NFE exome

AF:

0.0169

Gnomad4 OTH exome

AF:

0.0257

GnomAD4 genome

AF:

0.0177

AC:

2700

AN:

152274

Hom.:

Cov.:

AF XY:

0.0185

AC XY:

1378

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.00313

Gnomad4 AMR

AF:

0.0267

Gnomad4 ASJ

AF:

0.0613

Gnomad4 EAS

AF:

0.000966

Gnomad4 SAS

AF:

0.0772

Gnomad4 FIN

AF:

0.00839

Gnomad4 NFE

AF:

0.0203

Gnomad4 OTH

AF:

0.0284

Alfa

AF:

0.0167

Hom.:

Bravo

AF:

0.0167

EpiCase

AF:

0.0273

EpiControl

AF:

0.0277

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.27

DANN

Benign

0.31

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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