Variant 4-47677925-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000273857.9(CORIN):c.1249+13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00694 in 1,570,902 control chromosomes in the GnomAD database, including 105 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 0.0053 ( 8 hom., cov: 32)

Exomes 𝑓: 0.0071 ( 97 hom. )

Consequence

CORIN
ENST00000273857.9 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.679

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00532 (810/152228) while in subpopulation SAS AF= 0.0241 (116/4816). AF 95% confidence interval is 0.0205. There are 8 homozygotes in gnomad4. There are 393 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 810 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
CORIN	NM_006587.4 linkuse as main transcript	c.1249+13C>T	intron_variant	ENST00000273857.9	NP_006578.2
CORIN	NM_001278585.2 linkuse as main transcript	c.937+13C>T	intron_variant		NP_001265514.1
CORIN	NM_001278586.2 linkuse as main transcript	c.1138+13C>T	intron_variant		NP_001265515.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CORIN	ENST00000273857.9 linkuse as main transcript	c.1249+13C>T		intron_variant		1	NM_006587.4	ENSP00000273857	P2	Q9Y5Q5-1

Frequencies

GnomAD3 genomes

AF:

0.00533

AC:

811

AN:

152110

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00111

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00386

Gnomad ASJ

AF:

0.0202

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0241

Gnomad FIN

AF:

0.00547

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00641

Gnomad OTH

AF:

0.00862

GnomAD3 exomes

AF:

0.00888

AC:

2223

AN:

250422

Hom.:

AF XY:

0.0102

AC XY:

1380

AN XY:

135302

show subpopulations

Gnomad AFR exome

AF:

0.00105

Gnomad AMR exome

AF:

0.00316

Gnomad ASJ exome

AF:

0.0146

Gnomad EAS exome

AF:

0.0000546

Gnomad SAS exome

AF:

0.0331

Gnomad FIN exome

AF:

0.00588

Gnomad NFE exome

AF:

0.00667

Gnomad OTH exome

AF:

0.00933

GnomAD4 exome

AF:

0.00711

AC:

10088

AN:

1418674

Hom.:

Cov.:

AF XY:

0.00776

AC XY:

5496

AN XY:

708498

show subpopulations

Gnomad4 AFR exome

AF:

0.000980

Gnomad4 AMR exome

AF:

0.00351

Gnomad4 ASJ exome

AF:

0.0146

Gnomad4 EAS exome

AF:

0.000152

Gnomad4 SAS exome

AF:

0.0300

Gnomad4 FIN exome

AF:

0.00560

Gnomad4 NFE exome

AF:

0.00567

Gnomad4 OTH exome

AF:

0.00809

GnomAD4 genome

AF:

0.00532

AC:

810

AN:

152228

Hom.:

Cov.:

AF XY:

0.00528

AC XY:

393

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.00111

Gnomad4 AMR

AF:

0.00386

Gnomad4 ASJ

AF:

0.0202

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0241

Gnomad4 FIN

AF:

0.00547

Gnomad4 NFE

AF:

0.00641

Gnomad4 OTH

AF:

0.00853

Alfa

AF:

0.00743

Hom.:

Bravo

AF:

0.00434

Asia WGS

AF:

0.0110

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.10

DANN

Benign

0.54

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