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NM_001166686.2(PFKM):c.5A>T (p.His2Leu)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jul 12, 2021)
Last evaluated:
Jul 1, 2021
Accession:
VCV000441153.4
Variation ID:
441153
Description:
single nucleotide variant
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NM_001166686.2(PFKM):c.5A>T (p.His2Leu)

Allele ID
434767
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q13.11
Genomic location
12: 48107378 (GRCh38) GRCh38 UCSC
12: 48501161 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.48501161A>T
NC_000012.12:g.48107378A>T
NM_001166686.2:c.5A>T NP_001160158.1:p.His2Leu missense
... more HGVS
Protein change
H2L
Other names
-
Canonical SPDI
NC_000012.12:48107377:A:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.35623 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.23437
Exome Aggregation Consortium (ExAC) 0.26633
The Genome Aggregation Database (gnomAD) 0.22425
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.18748
1000 Genomes Project 0.35623
The Genome Aggregation Database (gnomAD), exomes 0.28169
Links
ClinGen: CA6536747
dbSNP: rs11609399
Varsome
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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 Jul 1, 2021 RCV001284933.2
Benign 2 criteria provided, single submitter Jun 14, 2018 RCV000509231.2

Clinical features observed in individuals with this variant

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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PFKM - - GRCh38
GRCh37
324 337

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jun 14, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000977361.1
Submitted: (Apr 12, 2019)
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)
Benign
(Aug 31, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type VII
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV001471032.1
Submitted: (Dec 11, 2020)
Evidence details
Benign
(Jul 01, 2021)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type VII
Allele origin: germline
Pars Genome Lab
Accession: SCV001750023.1
Submitted: (Jul 12, 2021)
Evidence details
not provided
(-)
no assertion provided
Method: phenotyping only
Not Provided
Allele origin: unknown
GenomeConnect, ClinGen
Accession: SCV000607357.1
Submitted: (Aug 22, 2017)
Evidence details
Comment:
GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical … (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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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 rs11609399...

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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 Jul 14, 2021