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NM_005334.3(HCFC1):c.2974G>A (p.Ala992Thr)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
2 (Most recent: Jan 29, 2020)
Last evaluated:
Dec 31, 2019
Accession:
VCV000445938.4
Variation ID:
445938
Description:
single nucleotide variant
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NM_005334.3(HCFC1):c.2974G>A (p.Ala992Thr)

Allele ID
439210
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 153955425 (GRCh38) GRCh38 UCSC
X: 153220876 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.153220876C>T
NC_000023.11:g.153955425C>T
NG_012513.1:g.20944G>A
NM_005334.3:c.2974G>A MANE Select NP_005325.2:p.Ala992Thr missense
Protein change
A992T
Other names
-
Canonical SPDI
NC_000023.11:153955424:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00053 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00095
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00019
The Genome Aggregation Database (gnomAD), exomes 0.00080
The Genome Aggregation Database (gnomAD) 0.00119
Trans-Omics for Precision Medicine (TOPMed) 0.00030
1000 Genomes Project 0.00053
Links
ClinGen: CA10557252
dbSNP: rs200997332
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 Jun 2, 2017 RCV000514364.4
Benign 1 criteria provided, single submitter Dec 31, 2019 RCV001089332.1
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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
349 597

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jun 02, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000610795.1
Submitted: (Oct 05, 2017)
Evidence details
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
Mental retardation 3, X-linked
Allele origin: germline
Invitae
Accession: SCV001118322.2
Submitted: (Jan 29, 2020)
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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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 rs200997332...

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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 Nov 20, 2021