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NM_006415.4(SPTLC1):c.1411G>A (p.Val471Ile)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Sep 24, 2021)
Last evaluated:
Nov 26, 2020
Accession:
VCV000287303.9
Variation ID:
287303
Description:
single nucleotide variant
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NM_006415.4(SPTLC1):c.1411G>A (p.Val471Ile)

Allele ID
271540
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q22.31
Genomic location
9: 92032476 (GRCh38) GRCh38 UCSC
9: 94794758 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.94794758C>T
NC_000009.12:g.92032476C>T
NG_007950.1:g.87933G>A
... more HGVS
Protein change
V471I, V316I, V349I, R460H
Other names
-
Canonical SPDI
NC_000009.12:92032475:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00379 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00074
1000 Genomes Project 0.00379
The Genome Aggregation Database (gnomAD), exomes 0.00067
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00192
The Genome Aggregation Database (gnomAD) 0.00217
Trans-Omics for Precision Medicine (TOPMed) 0.00224
Trans-Omics for Precision Medicine (TOPMed) 0.00280
The Genome Aggregation Database (gnomAD) 0.00272
Links
ClinGen: CA5121185
dbSNP: rs141292904
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 Mar 26, 2020 RCV000756719.6
Benign 1 criteria provided, single submitter Nov 26, 2020 RCV000290677.5
Benign 1 criteria provided, single submitter May 13, 2016 RCV000405876.4
Likely benign 1 criteria provided, single submitter - RCV001174091.1
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV001249810.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SPTLC1 - - GRCh38
GRCh37
216 249

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(May 13, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000341037.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
http://www.ncbi.nlm.nih.gov/vari…
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Hereditary Sensory and Autonomic Neuropathy, Type IA
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000481048.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jun 14, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000884609.1
Submitted: (Oct 10, 2018)
Evidence details
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
Charcot-Marie-Tooth disease
Allele origin: germline
Molecular Genetics Laboratory,London Health Sciences Centre
Accession: SCV001337212.1
Submitted: (Apr 07, 2020)
Evidence details
Benign
(Nov 26, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary sensory and autonomic neuropathy type 1
Allele origin: germline
Invitae
Accession: SCV000752342.4
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Mar 26, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000516667.4
Submitted: (Sep 24, 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.

Text-mined citations for rs141292904...

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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 Nov 27, 2021