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NM_001127671.2(LIFR):c.1915A>T (p.Met639Leu)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Aug 13, 2021)
Last evaluated:
Dec 6, 2020
Accession:
VCV000353622.8
Variation ID:
353622
Description:
single nucleotide variant
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NM_001127671.2(LIFR):c.1915A>T (p.Met639Leu)

Allele ID
303919
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5p13.1
Genomic location
5: 38493756 (GRCh38) GRCh38 UCSC
5: 38493858 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.10:g.38493756T>A
NC_000005.9:g.38493858T>A
NG_011817.1:g.106650A>T
... more HGVS
Protein change
M639L
Other names
-
Canonical SPDI
NC_000005.10:38493755:T:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00659 (A)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00054
The Genome Aggregation Database (gnomAD) 0.00064
Trans-Omics for Precision Medicine (TOPMed) 0.00053
The Genome Aggregation Database (gnomAD), exomes 0.00227
Exome Aggregation Consortium (ExAC) 0.00264
1000 Genomes Project 0.00659
Links
dbSNP: rs143808825
ClinGen: CA3242807
VarSome
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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 Dec 6, 2020 RCV000970444.5
Benign 2 criteria provided, single submitter Jan 12, 2018 RCV000383609.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
LIFR - - GRCh38
GRCh37
516 548

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Stüve-Wiedemann syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000457589.3
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)
Likely benign
(Oct 16, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001783396.1
Submitted: (Aug 13, 2021)
Evidence details
Benign
(Dec 06, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001118021.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jan 12, 2020)
no assertion criteria provided
Method: clinical testing
Stuve-Wiedemann syndrome
Allele origin: germline
Natera, Inc.
Accession: SCV001452990.1
Submitted: (Dec 28, 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 rs143808825...

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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 Sep 23, 2021