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NM_001081.4(CUBN):c.10245C>T (p.Tyr3415=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
2 (Most recent: Feb 20, 2020)
Last evaluated:
Dec 31, 2019
Accession:
VCV000299365.4
Variation ID:
299365
Description:
single nucleotide variant
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NM_001081.4(CUBN):c.10245C>T (p.Tyr3415=)

Allele ID
309867
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10p13
Genomic location
10: 16835131 (GRCh38) GRCh38 UCSC
10: 16877130 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_001081.3:c.10245C>T NP_001072.2:p.Tyr3415= synonymous
LRG_540:g.299687C>T
LRG_540t1:c.10245C>T LRG_540p1:p.Tyr3415=
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000010.11:16835130:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00035
Exome Aggregation Consortium (ExAC) 0.00046
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00054
Trans-Omics for Precision Medicine (TOPMed) 0.00088
1000 Genomes Project 0.00080
The Genome Aggregation Database (gnomAD) 0.00067
Links
ClinGen: CA5422431
dbSNP: rs147730705
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 RCV000321124.2
Benign 1 criteria provided, single submitter Dec 31, 2019 RCV000861380.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CUBN - - GRCh38
GRCh37
923 945

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
Juvenile type megaloblastic anemia
Allele origin: germline
Invitae
Accession: SCV001001680.2
Submitted: (Jan 29, 2020)
Evidence details
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Imerslund-Gräsbeck syndrome 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000361606.3
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 rs147730705...

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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 24, 2021