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_002299.4(LCT):c.1539G>A (p.Glu513=)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jul 4, 2021)
Last evaluated:
Feb 1, 2021
Accession:
VCV000893076.4
Variation ID:
893076
Description:
single nucleotide variant
Help

NM_002299.4(LCT):c.1539G>A (p.Glu513=)

Allele ID
881095
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q21.3
Genomic location
2: 135817509 (GRCh38) GRCh38 UCSC
2: 136575079 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_338:g.42661G>A
LRG_338t1:c.1539G>A
NC_000002.11:g.136575079C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:135817508:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00067
The Genome Aggregation Database (gnomAD) 0.00054
Trans-Omics for Precision Medicine (TOPMed) 0.00053
Trans-Omics for Precision Medicine (TOPMed) 0.00062
The Genome Aggregation Database (gnomAD), exomes 0.00072
1000 Genomes Project 0.00020
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00023
Links
dbSNP: rs202186209
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Feb 1, 2021 RCV001520844.2
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001130286.2
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
LCT - - GRCh38
GRCh37
184 199

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Congenital lactase deficiency
Affected status: unknown
Allele origin: germline
Illumina Laboratory Services,Illumina
Accession: SCV001289857.1
Submitted: (Feb 20, 2020)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)

Observation 1:

Observation 2:

Benign
(Oct 25, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV001730055.1
Submitted: (Jan 07, 2021)
Likely benign
(Feb 01, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
Affected status: yes
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001747961.1
Submitted: (Jul 04, 2021)
Number of individuals with the variant: 1

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
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 rs202186209...

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 Jan 08, 2022