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NM_025077.4(TOE1):c.52+77G>A

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Mar 31, 2021)
Last evaluated:
Apr 27, 2017
Accession:
VCV000428279.5
Variation ID:
428279
Description:
single nucleotide variant
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NM_025077.4(TOE1):c.52+77G>A

Allele ID
419304
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p34.1
Genomic location
1: 45340381 (GRCh38) GRCh38 UCSC
1: 45806053 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_001128425.1:c.-127C>T 5 prime UTR
LRG_220:g.5090C>T
LRG_220t1:c.-127C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:45340380:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00938 (A)

Allele frequency
1000 Genomes Project 0.00938
Trans-Omics for Precision Medicine (TOPMed) 0.02110
The Genome Aggregation Database (gnomAD) 0.02329
Links
ClinGen: CA10670682
dbSNP: rs3219466
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 10, 2013 RCV000491011.2
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV001097391.1
Uncertain significance 1 no assertion criteria provided - RCV000504244.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MUTYH - - GRCh38
GRCh37
1650 1755
TOE1 - - GRCh38
GRCh37
41 146

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jan 10, 2013)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000580076.4
Submitted: (Nov 30, 2020)
Evidence details
Comment:
There is insufficient or conflicting evidence for classification of this alteration.
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
MYH-associated polyposis
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001253669.1
Submitted: (Feb 20, 2020)
Evidence details
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)
Uncertain significance
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV000592670.2
Submitted: (Mar 31, 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 rs3219466...

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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 20, 2021