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NM_003126.4(SPTA1):c.3160A>T (p.Thr1054Ser)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(1);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Feb 20, 2020)
Last evaluated:
Dec 24, 2018
Accession:
VCV000293001.3
Variation ID:
293001
Description:
single nucleotide variant
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NM_003126.4(SPTA1):c.3160A>T (p.Thr1054Ser)

Allele ID
276718
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q23.1
Genomic location
1: 158653302 (GRCh38) GRCh38 UCSC
1: 158623092 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.11:g.158653302T>A
NC_000001.10:g.158623092T>A
NM_003126.4:c.3160A>T MANE Select NP_003117.2:p.Thr1054Ser missense
... more HGVS
Protein change
T1054S
Other names
-
Canonical SPDI
NC_000001.11:158653301:T:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00499 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00110
Exome Aggregation Consortium (ExAC) 0.00138
The Genome Aggregation Database (gnomAD) 0.00392
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00455
Trans-Omics for Precision Medicine (TOPMed) 0.00485
1000 Genomes Project 0.00499
Links
ClinGen: CA1183157
dbSNP: rs145054175
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000278510.2
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000335941.2
Likely benign 1 criteria provided, single submitter Jan 12, 2018 RCV000405289.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 24, 2018 RCV000756700.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SPTA1 - - GRCh38
GRCh37
436 477

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Nov 29, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV000884590.1
Submitted: (Oct 10, 2018)
Evidence details
Benign
(Dec 24, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001121844.1
Submitted: (Mar 14, 2019)
Evidence details
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary pyropoikilocytosis
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000349421.3
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
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Elliptocytosis 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000349422.3
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)
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Spherocytosis type 3
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000349420.3
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)

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 rs145054175...

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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 Apr 08, 2021