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NM_005477.3(HCN4):c.3117G>A (p.Pro1039=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Sep 28, 2021)
Last evaluated:
Nov 3, 2020
Accession:
VCV000412793.7
Variation ID:
412793
Description:
single nucleotide variant
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NM_005477.3(HCN4):c.3117G>A (p.Pro1039=)

Allele ID
400332
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q24.1
Genomic location
15: 73322976 (GRCh38) GRCh38 UCSC
15: 73615317 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.73322976C>T
NC_000015.9:g.73615317C>T
NG_009063.1:g.51289G>A
NM_005477.3:c.3117G>A MANE Select NP_005468.1:p.Pro1039= synonymous
Protein change
-
Other names
-
Canonical SPDI
NC_000015.10:73322975:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00028
The Genome Aggregation Database (gnomAD) 0.00036
The Genome Aggregation Database (gnomAD), exomes 0.00046
Exome Aggregation Consortium (ExAC) 0.00071
Links
ClinGen: CA7648881
dbSNP: rs749785521
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Mar 11, 2017 RCV000618514.1
Likely benign 1 criteria provided, single submitter Nov 3, 2020 RCV001084471.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jan 24, 2020 RCV000594205.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
HCN4 - - GRCh38
GRCh37
781 815

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Nov 03, 2020)
criteria provided, single submitter
Method: clinical testing
Brugada syndrome 8
Allele origin: germline
Invitae
Accession: SCV000554502.5
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Oct 13, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000702751.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Mar 11, 2017)
criteria provided, single submitter
Method: clinical testing
Cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000737928.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Synonymous alterations with insufficient evidence to classify as benign
Likely benign
(Jan 24, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001946331.1
Submitted: (Sep 28, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=HCN4 - - - -

Text-mined citations for rs749785521...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2021