4-47603404-G-T
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_006587.4(CORIN):c.2805C>A(p.Gly935Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00239 in 1,613,732 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.011 ( 32 hom., cov: 32)
Exomes 𝑓: 0.0015 ( 32 hom. )
Consequence
CORIN
NM_006587.4 synonymous
NM_006587.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.36
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 -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
Variant 4-47603404-G-T is Benign according to our data. Variant chr4-47603404-G-T is described in ClinVar as [Benign]. Clinvar id is 785089.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=2.36 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0113 (1718/152194) while in subpopulation AFR AF= 0.0383 (1591/41516). AF 95% confidence interval is 0.0368. There are 32 homozygotes in gnomad4. There are 808 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1718 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CORIN | NM_006587.4 | c.2805C>A | p.Gly935Gly | synonymous_variant | 20/22 | ENST00000273857.9 | NP_006578.2 | |
CORIN | NM_001278585.2 | c.2493C>A | p.Gly831Gly | synonymous_variant | 18/20 | NP_001265514.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CORIN | ENST00000273857.9 | c.2805C>A | p.Gly935Gly | synonymous_variant | 20/22 | 1 | NM_006587.4 | ENSP00000273857.4 |
Frequencies
GnomAD3 genomes AF: 0.0113 AC: 1713AN: 152076Hom.: 31 Cov.: 32
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GnomAD3 exomes AF: 0.00374 AC: 930AN: 248368Hom.: 15 AF XY: 0.00290 AC XY: 390AN XY: 134352
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GnomAD4 exome AF: 0.00146 AC: 2140AN: 1461538Hom.: 32 Cov.: 32 AF XY: 0.00125 AC XY: 908AN XY: 727066
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GnomAD4 genome AF: 0.0113 AC: 1718AN: 152194Hom.: 32 Cov.: 32 AF XY: 0.0109 AC XY: 808AN XY: 74394
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at