rs75770792
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006587.4(CORIN):c.1664C>T(p.Thr555Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00333 in 1,613,568 control chromosomes in the GnomAD database, including 168 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.018 ( 93 hom., cov: 32)
Exomes 𝑓: 0.0018 ( 75 hom. )
Consequence
CORIN
NM_006587.4 missense
NM_006587.4 missense
Scores
2
6
10
Clinical Significance
Conservation
PhyloP100: 7.25
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.007813364).
BP6
?
Variant 4-47661782-G-A is Benign according to our data. Variant chr4-47661782-G-A is described in ClinVar as [Benign]. Clinvar id is 785091.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0618 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CORIN | NM_006587.4 | c.1664C>T | p.Thr555Ile | missense_variant | 12/22 | ENST00000273857.9 | |
CORIN | NM_001278585.2 | c.1352C>T | p.Thr451Ile | missense_variant | 10/20 | ||
CORIN | NM_001278586.2 | c.1553C>T | p.Thr518Ile | missense_variant | 11/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CORIN | ENST00000273857.9 | c.1664C>T | p.Thr555Ile | missense_variant | 12/22 | 1 | NM_006587.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0184 AC: 2797AN: 152194Hom.: 93 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00456 AC: 1144AN: 250680Hom.: 28 AF XY: 0.00337 AC XY: 456AN XY: 135466
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GnomAD4 exome AF: 0.00176 AC: 2579AN: 1461256Hom.: 75 Cov.: 31 AF XY: 0.00148 AC XY: 1075AN XY: 726916
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GnomAD4 genome ? AF: 0.0184 AC: 2799AN: 152312Hom.: 93 Cov.: 32 AF XY: 0.0181 AC XY: 1351AN XY: 74484
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ExAC
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695
Asia WGS
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3478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;.;T;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D;D
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.;.;.;.
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;N;N;N;D
REVEL
Uncertain
Sift
Benign
T;.;D;D;D;T
Sift4G
Pathogenic
D;D;D;D;D;D
Polyphen
D;.;.;.;.;.
Vest4
MVP
MPC
ClinPred
T
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at