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NM_000214.3(JAG1):c.2043G>A (p.Thr681=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 21, 2020
Accession:
VCV000499978.6
Variation ID:
499978
Description:
single nucleotide variant
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NM_000214.3(JAG1):c.2043G>A (p.Thr681=)

Allele ID
491402
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
20p12.2
Genomic location
20: 10645426 (GRCh38) GRCh38 UCSC
20: 10626074 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_1191:g.33621G>A
LRG_1191t1:c.2043G>A LRG_1191p1:p.Thr681=
NC_000020.10:g.10626074C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000020.11:10645425:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00010
Trans-Omics for Precision Medicine (TOPMed) 0.00029
Exome Aggregation Consortium (ExAC) 0.00012
1000 Genomes Project 0.00020
Trans-Omics for Precision Medicine (TOPMed) 0.00024
The Genome Aggregation Database (gnomAD) 0.00026
The Genome Aggregation Database (gnomAD) 0.00029
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00054
Links
ClinGen: CA9764662
dbSNP: rs151291264
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 Aug 7, 2018 RCV000596723.4
Likely benign 1 criteria provided, single submitter Nov 10, 2016 RCV000618168.1
Likely benign 1 criteria provided, single submitter Nov 21, 2020 RCV001089168.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
JAG1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
870 901

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Aug 07, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000705729.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Nov 10, 2016)
criteria provided, single submitter
Method: clinical testing
Cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000735612.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Synonymous alterations with insufficient evidence to classify as benign
Likely benign
(Nov 21, 2020)
criteria provided, single submitter
Method: clinical testing
Alagille syndrome 1
Allele origin: germline
Invitae
Accession: SCV001005940.3
Submitted: (Jan 07, 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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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=JAG1 - - - -

Text-mined citations for rs151291264...

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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