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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
ClinVar Genomic variation as it relates to human health
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- Interpretation:
-
Benign
- Review status:
- criteria provided, multiple submitters, no conflicts
- Submissions:
- 10
- First in ClinVar:
- Feb 20, 2014
- Most recent Submission:
- May 16, 2022
- Last evaluated:
- Dec 10, 2021
- Accession:
- VCV000098207.14
- Variation ID:
- 98207
- Description:
- single nucleotide variant
Help
NM_001377265.1(MAPT):c.1857A>G (p.Ala619=)
- Allele ID
- 104099
- Variant type
- single nucleotide variant
- Variant length
- 1 bp
- Cytogenetic location
- 17q21.31
- Genomic location
- 17: 45996523 (GRCh38) GRCh38 UCSC
- 17: 44073889 (GRCh37) GRCh37 UCSC
- HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001377265.1:c.1857A>G MANE Select NP_001364194.1:p.Ala619= synonymous NM_001123066.4:c.1686A>G NP_001116538.2:p.Ala562= synonymous NM_001123067.4:c.594A>G NP_001116539.1:p.Ala198= synonymous NM_001203251.2:c.594A>G NP_001190180.1:p.Ala198= synonymous NM_001203252.2:c.681A>G NP_001190181.1:p.Ala227= synonymous NM_001377266.1:c.1659A>G NP_001364195.1:p.Ala553= synonymous NM_001377267.1:c.594A>G NP_001364196.1:p.Ala198= synonymous NM_001377268.1:c.507A>G NP_001364197.1:p.Ala169= synonymous NM_005910.6:c.681A>G NP_005901.2:p.Ala227= synonymous NM_016834.5:c.507A>G NP_058518.1:p.Ala169= synonymous NM_016835.5:c.1632A>G NP_058519.3:p.Ala544= synonymous NM_016841.5:c.507A>G NP_058525.1:p.Ala169= synonymous NR_165166.1:n.605A>G NC_000017.11:g.45996523A>G NC_000017.10:g.44073889A>G NG_007398.1:g.107103A>G NG_007398.2:g.107061A>G LRG_660:g.107061A>G LRG_660t1:c.1632A>G LRG_660p1:p.Ala544= LRG_660t2:c.1857A>G LRG_660p2:p.Ala619= - Protein change
- -
- Other names
- -
- Canonical SPDI
- NC_000017.11:45996522:A:G
- Functional consequence
- -
- Global minor allele frequency (GMAF)
- 0.08826 (G)
- Allele frequency
- 1000 Genomes Project 0.08826
- Exome Aggregation Consortium (ExAC) 0.14580
- Trans-Omics for Precision Medicine (TOPMed) 0.15055
- The Genome Aggregation Database (gnomAD) 0.12790
- The Genome Aggregation Database (gnomAD), exomes 0.14464
- The Genome Aggregation Database (gnomAD) 0.14782
- Trans-Omics for Precision Medicine (TOPMed) 0.15029
- NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.16392
- Links
- ClinGen: CA225407
- dbSNP: rs1052553
- VarSome
Help
Aggregate interpretations per condition
| Interpreted condition | Interpretation | Number of submissions | Review status | Last evaluated | Variation/condition record |
|---|---|---|---|---|---|
| Benign | 6 | criteria provided, multiple submitters, no conflicts | Feb 25, 2011 | RCV000243822.7 | |
| Benign | 2 | criteria provided, single submitter | Aug 11, 2018 | RCV000084512.3 | |
| Benign | 1 | criteria provided, single submitter | Jan 13, 2018 | RCV000295833.3 | |
| Benign | 1 | criteria provided, single submitter | Dec 10, 2021 | RCV001510740.4 |
Submitted interpretations and evidence
Help| Interpretation (Last evaluated) |
Review status (Assertion criteria) |
Condition (Inheritance) |
Submitter | More information | |
|---|---|---|---|---|---|
|
Benign
(-)
|
criteria provided, single submitter
Method: clinical testing
|
NOT SPECIFIED
Affected status: unknown
Allele origin:
germline
|
PreventionGenetics,PreventionGenetics
Accession: SCV000306670.1
First in ClinVar: Oct 02, 2016 Last updated: Oct 02, 2016 |
|
|
|
Benign
(Feb 25, 2011)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Athena Diagnostics Inc
Accession: SCV000614046.1
First in ClinVar: Oct 02, 2016 Last updated: Oct 02, 2016 |
|
|
|
Benign
(Dec 10, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Frontotemporal dementia
Affected status: unknown
Allele origin:
germline
|
Invitae
Accession: SCV001717850.2
First in ClinVar: Jun 15, 2021 Last updated: May 16, 2022 |
|
|
|
Benign
(Jan 13, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
MAPT-Related Spectrum Disorders
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services,Illumina
Accession: SCV000403484.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
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)
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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
|
|
|
Benign
(Aug 11, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV001873336.1
First in ClinVar: Sep 19, 2021 Last updated: Sep 19, 2021 |
|
|
|
Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001808841.1 First in ClinVar: Aug 25, 2021 Last updated: Aug 25, 2021 |
|
|
|
Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
Clinical Genetics, Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001918497.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021 |
|
|
|
Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001959277.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
|
|
|
Benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001967329.1 First in ClinVar: Oct 07, 2021 Last updated: Oct 07, 2021 |
|
|
|
not provided
(-)
|
no assertion provided
Method: not provided
|
not provided
Affected status: not provided
Allele origin:
not provided
|
VIB Department of Molecular Genetics, University of Antwerp
Accession: SCV000116648.1
First in ClinVar: Feb 20, 2014 Last updated: Feb 20, 2014
Comment:
http://phencode.bx.psu.edu/cgi-bin/phencode/phencode?build=hg18&id=ADM_219
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Functional evidence
Help| 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
Help| 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 rs1052553...
HelpThese 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 Aug 24, 2022