chr4-47786656-G-A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_006587.4(CORIN):​c.409+69C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00069 in 1,214,422 control chromosomes in the GnomAD database, including 2 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 0.0033 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00032 ( 0 hom. )

Consequence

CORIN
NM_006587.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.31

Publications

1 publications found
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 Gene-Disease associations (from GenCC):
  • preeclampsia/eclampsia 5
    Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BS2
High Homozygotes in GnomAd4 at 2 Unknown gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CORINNM_006587.4 linkc.409+69C>T intron_variant Intron 3 of 21 ENST00000273857.9 NP_006578.2 Q9Y5Q5-1B4E2W9
CORINNM_001278585.2 linkc.208+20247C>T intron_variant Intron 2 of 19 NP_001265514.1 Q9Y5Q5A0A087X1D5B4E1Y7B4E2W9
CORINNM_001278586.2 linkc.409+69C>T intron_variant Intron 3 of 13 NP_001265515.1 J3KR83B4E2W9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CORINENST00000273857.9 linkc.409+69C>T intron_variant Intron 3 of 21 1 NM_006587.4 ENSP00000273857.4 Q9Y5Q5-1

Frequencies

GnomAD3 genomes
AF:
0.00326
AC:
496
AN:
152160
Hom.:
2
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0116
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000589
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000208
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00191
GnomAD4 exome
AF:
0.000321
AC:
341
AN:
1062144
Hom.:
0
AF XY:
0.000290
AC XY:
157
AN XY:
541406
show subpopulations
African (AFR)
AF:
0.0120
AC:
296
AN:
24734
American (AMR)
AF:
0.000305
AC:
11
AN:
36042
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
21272
East Asian (EAS)
AF:
0.00
AC:
0
AN:
37620
South Asian (SAS)
AF:
0.00
AC:
0
AN:
71036
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
51788
Middle Eastern (MID)
AF:
0.000621
AC:
3
AN:
4830
European-Non Finnish (NFE)
AF:
0.00000130
AC:
1
AN:
767864
Other (OTH)
AF:
0.000639
AC:
30
AN:
46958
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
18
36
55
73
91
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
10
20
30
40
50
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.00326
AC:
497
AN:
152278
Hom.:
2
Cov.:
32
AF XY:
0.00289
AC XY:
215
AN XY:
74460
show subpopulations
African (AFR)
AF:
0.0116
AC:
483
AN:
41564
American (AMR)
AF:
0.000589
AC:
9
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3472
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5180
South Asian (SAS)
AF:
0.000208
AC:
1
AN:
4812
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10616
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
68024
Other (OTH)
AF:
0.00189
AC:
4
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
26
51
77
102
128
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
10
20
30
40
50
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00184
Hom.:
0
Bravo
AF:
0.00385
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
0.14
DANN
Benign
0.66
PhyloP100
-1.3

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

Other links and lift over

dbSNP: rs74701656; hg19: chr4-47788673; API