4-47686047-A-G

Position:

• chr4-47686047-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006587.4(CORIN):​c.914-2209T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 145,064 control chromosomes in the GnomAD database, including 20,798 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 0.53 (20798 hom., cov: 21)
• Consequence: CORIN NM_006587.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CORIN	NM_006587.4	c.914-2209T>C		intron_variant		ENST00000273857.9	NP_006578.2
CORIN	NM_001278585.2	c.713-2209T>C		intron_variant			NP_001265514.1
CORIN	NM_001278586.2	c.914-2209T>C		intron_variant			NP_001265515.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CORIN	ENST00000273857.9	c.914-2209T>C		intron_variant		1	NM_006587.4	ENSP00000273857.4

Frequencies

GnomAD3 genomes AF: 0.527 AC: 76330 AN: 144946 Hom.: 20781 Cov.: 21

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.517

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.526 AC: 76375 AN: 145064 Hom.: 20798 Cov.: 21 AF XY: 0.520 AC XY: 36539 AN XY: 70238

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.510

Alfa AF: 0.569 Hom.: 48748

Bravo AF: 0.523

Asia WGS AF: 0.329 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.38
DANN	Benign	0.30

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

Other links and lift over

dbSNP: rs7661217; hg19: chr4-47688064;