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NM_005477.3(HCN4):c.2701G>A (p.Ala901Thr)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Sep 30, 2021)
Last evaluated:
Jul 26, 2021
Accession:
VCV000404120.9
Variation ID:
404120
Description:
single nucleotide variant
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NM_005477.3(HCN4):c.2701G>A (p.Ala901Thr)

Allele ID
400342
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q24.1
Genomic location
15: 73323392 (GRCh38) GRCh38 UCSC
15: 73615733 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.73323392C>T
NC_000015.9:g.73615733C>T
NG_009063.1:g.50873G>A
NM_005477.3:c.2701G>A MANE Select NP_005468.1:p.Ala901Thr missense
Protein change
A901T
Other names
-
Canonical SPDI
NC_000015.10:73323391:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00013
The Genome Aggregation Database (gnomAD) 0.00016
Exome Aggregation Consortium (ExAC) 0.00026
Trans-Omics for Precision Medicine (TOPMed) 0.00011
1000 Genomes Project 0.00040
Links
ClinGen: CA7648968
dbSNP: rs201742383
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 Oct 13, 2020 RCV000464894.7
Uncertain significance 1 criteria provided, single submitter Jul 26, 2021 RCV000480340.2
Likely benign 1 criteria provided, single submitter Jan 17, 2019 RCV000619580.1
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV001118937.1
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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
(Jan 17, 2019)
criteria provided, single submitter
Method: clinical testing
Cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000737765.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Subpopulation frequency in support of benign classification
Likely benign
(Oct 13, 2020)
criteria provided, single submitter
Method: clinical testing
Brugada syndrome 8
Allele origin: germline
Invitae
Accession: SCV000541553.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Jul 26, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000574427.4
Submitted: (Sep 30, 2021)
Evidence details
Comment:
Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant does not alter protein structure/function; … (more)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Sick sinus syndrome 2, autosomal dominant
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001277258.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)

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
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs201742383...

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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