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NM_002299.4(LCT):c.655G>A (p.Val219Ile)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Sep 30, 2021)
Last evaluated:
Dec 5, 2020
Accession:
VCV000331207.7
Variation ID:
331207
Description:
single nucleotide variant
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NM_002299.4(LCT):c.655G>A (p.Val219Ile)

Allele ID
281884
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q21.3
Genomic location
2: 135833176 (GRCh38) GRCh38 UCSC
2: 136590746 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P09848:p.Val219Ile
LRG_338t1:c.655G>A
LRG_338:g.26994G>A
... more HGVS
Protein change
V219I
Other names
-
Canonical SPDI
NC_000002.12:135833175:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.35503 (T)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.27026
Trans-Omics for Precision Medicine (TOPMed) 0.28822
1000 Genomes Project 0.35503
Links
ClinGen: CA1888576
UniProtKB: P09848#VAR_026705
dbSNP: rs3754689
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 Dec 5, 2020 RCV001509608.4
Benign 1 criteria provided, single submitter Jun 14, 2016 RCV000288474.2
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000382944.2
Benign 2 no assertion criteria provided - RCV001701856.2
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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

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Lactose Intolerance
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000416534.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Congenital lactase deficiency
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000416533.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001716429.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Nov 12, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001850503.1
Submitted: (Sep 10, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 27060170)
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001932561.1
Submitted: (Sep 23, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001959657.1
Submitted: (Sep 30, 2021)
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 rs3754689...

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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 Oct 02, 2021