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NM_005334.3(HCFC1):c.3846G>A (p.Ser1282=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
2 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 14, 2020
Accession:
VCV000435397.4
Variation ID:
435397
Description:
single nucleotide variant
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NM_005334.3(HCFC1):c.3846G>A (p.Ser1282=)

Allele ID
430701
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 153954553 (GRCh38) GRCh38 UCSC
X: 153220004 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.153220004C>T
NC_000023.11:g.153954553C>T
NG_012513.1:g.21816G>A
NM_005334.3:c.3846G>A MANE Select NP_005325.2:p.Ser1282= synonymous
Protein change
-
Other names
-
Canonical SPDI
NC_000023.11:153954552:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00053 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00009
Exome Aggregation Consortium (ExAC) 0.00012
1000 Genomes Project 0.00053
The Genome Aggregation Database (gnomAD) 0.00005
Links
ClinGen: CA10557126
dbSNP: rs372301724
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Aug 22, 2016 RCV000503750.3
Likely benign 1 criteria provided, single submitter Nov 14, 2020 RCV001399716.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
HCFC1 - - GRCh38
GRCh37
356 604

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Uncertain significance
(Aug 22, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Affected status: no
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000595100.1
Submitted: (Jul 05, 2017)
Likely benign
(Nov 14, 2020)
criteria provided, single submitter
Method: clinical testing
Methylmalonic acidemia with homocystinuria, type cblX
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV001601512.1
Submitted: (Jan 07, 2021)

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs372301724...

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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 Jan 22, 2022