Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_005334.3(HCFC1):c.4545G>A (p.Pro1515=)

Help
Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 30, 2020
Accession:
VCV000167165.2
Variation ID:
167165
Description:
single nucleotide variant
Help

NM_005334.3(HCFC1):c.4545G>A (p.Pro1515=)

Allele ID
177762
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 153952911 (GRCh38) GRCh38 UCSC
X: 153218362 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.153218362C>T
NC_000023.11:g.153952911C>T
NM_005334.3:c.4545G>A MANE Select NP_005325.2:p.Pro1515= synonymous
NG_012513.1:g.23458G>A
Protein change
-
Other names
-
Canonical SPDI
NC_000023.11:153952910:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.03470 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.01514
Trans-Omics for Precision Medicine (TOPMed) 0.03501
1000 Genomes Project 0.03470
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.03293
The Genome Aggregation Database (gnomAD) 0.02952
Links
ClinGen: CA180101
dbSNP: rs1051153
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts Mar 8, 2016 RCV000153347.4
Benign 1 criteria provided, single submitter Nov 30, 2020 RCV001510628.1
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
HCFC1 - - GRCh38
GRCh37
331 579

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Mar 19, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000202831.7
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Nov 30, 2020)
criteria provided, single submitter
Method: clinical testing
Mental retardation 3, X-linked
Allele origin: germline
Invitae
Accession: SCV001717719.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Mar 08, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000521833.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)

Functional evidence

Help
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

Help
Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=HCFC1 - - - -

Text-mined citations for rs1051153...

Help
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 Jun 14, 2021