This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
ClinVar Genomic variation as it relates to human health
NM_000368.5(TSC1):c.3480T>C (p.His1160=)
Germline
Classification
Help
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
(2)
Help
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Likely benign
2
criteria provided, multiple submitters, no conflicts
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000368.5(TSC1):c.3480T>C (p.His1160=)
Variation ID: 1731846 Accession: VCV001731846.3
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 9q34.13 9: 132896250 (GRCh38) [ NCBI UCSC ] 9: 135771637 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Nov 29, 2022 May 1, 2024 Dec 31, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000368.5:c.3480T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000359.1:p.His1160= synonymous NM_001162426.2:c.3477T>C NP_001155898.1:p.His1159= synonymous NM_001162427.2:c.3327T>C NP_001155899.1:p.His1109= synonymous NM_001362177.2:c.3117T>C NP_001349106.1:p.His1039= synonymous NM_001406592.1:c.3480T>C NP_001393521.1:p.His1160= synonymous NM_001406593.1:c.3480T>C NP_001393522.1:p.His1160= synonymous NM_001406594.1:c.3480T>C NP_001393523.1:p.His1160= synonymous NM_001406595.1:c.3480T>C NP_001393524.1:p.His1160= synonymous NM_001406596.1:c.3480T>C NP_001393525.1:p.His1160= synonymous NM_001406597.1:c.3477T>C NP_001393526.1:p.His1159= synonymous NM_001406598.1:c.3477T>C NP_001393527.1:p.His1159= synonymous NM_001406599.1:c.3477T>C NP_001393528.1:p.His1159= synonymous NM_001406600.1:c.3477T>C NP_001393529.1:p.His1159= synonymous NM_001406601.1:c.3465T>C NP_001393530.1:p.His1155= synonymous NM_001406602.1:c.3465T>C NP_001393531.1:p.His1155= synonymous NM_001406603.1:c.3462T>C NP_001393532.1:p.His1154= synonymous NM_001406604.1:c.3462T>C NP_001393533.1:p.His1154= synonymous NM_001406605.1:c.3438T>C NP_001393534.1:p.His1146= synonymous NM_001406606.1:c.3438T>C NP_001393535.1:p.His1146= synonymous NM_001406607.1:c.3438T>C NP_001393536.1:p.His1146= synonymous NM_001406608.1:c.3435T>C NP_001393537.1:p.His1145= synonymous NM_001406609.1:c.3435T>C NP_001393538.1:p.His1145= synonymous NM_001406610.1:c.3327T>C NP_001393539.1:p.His1109= synonymous NM_001406611.1:c.3324T>C NP_001393540.1:p.His1108= synonymous NM_001406612.1:c.3324T>C NP_001393541.1:p.His1108= synonymous NM_001406613.1:c.3282T>C NP_001393542.1:p.His1094= synonymous NM_001406614.1:c.3117T>C NP_001393543.1:p.His1039= synonymous NM_001406615.1:c.3117T>C NP_001393544.1:p.His1039= synonymous NM_001406616.1:c.3117T>C NP_001393545.1:p.His1039= synonymous NM_001406617.1:c.3117T>C NP_001393546.1:p.His1039= synonymous NM_001406618.1:c.3117T>C NP_001393547.1:p.His1039= synonymous NM_001406619.1:c.3117T>C NP_001393548.1:p.His1039= synonymous NM_001406620.1:c.3114T>C NP_001393549.1:p.His1038= synonymous NM_001406621.1:c.3114T>C NP_001393550.1:p.His1038= synonymous NM_001406622.1:c.3114T>C NP_001393551.1:p.His1038= synonymous NM_001406623.1:c.3114T>C NP_001393552.1:p.His1038= synonymous NM_001406624.1:c.3075T>C NP_001393553.1:p.His1025= synonymous NM_001406625.1:c.3072T>C NP_001393554.1:p.His1024= synonymous NM_001406626.1:c.2529T>C NP_001393555.1:p.His843= synonymous NM_001406627.1:c.2526T>C NP_001393556.1:p.His842= synonymous NM_001406628.1:c.2526T>C NP_001393557.1:p.His842= synonymous NM_001406629.1:c.2427T>C NP_001393558.1:p.His809= synonymous NM_001406630.1:c.2427T>C NP_001393559.1:p.His809= synonymous NR_176214.1:n.3530T>C non-coding transcript variant NR_176215.1:n.3692T>C non-coding transcript variant NR_176216.1:n.3559T>C non-coding transcript variant NR_176217.1:n.3689T>C non-coding transcript variant NR_176218.1:n.3693T>C non-coding transcript variant NC_000009.12:g.132896250A>G NC_000009.11:g.135771637A>G NG_012386.1:g.53384T>C LRG_486:g.53384T>C LRG_486t1:c.3480T>C LRG_486p1:p.His1160= - Protein change
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- Other names
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- Canonical SPDI
- NC_000009.12:132896249:A:G
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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- Links
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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| TSC1 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
4843 | 4901 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Likely benign (1) |
criteria provided, single submitter
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Dec 31, 2023 | RCV003614106.2 | |
| Likely benign (1) |
criteria provided, single submitter
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May 7, 2021 | RCV002457372.2 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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|---|---|---|---|---|---|
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Likely benign
(Dec 31, 2023)
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criteria provided, single submitter
Method: clinical testing
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Tuberous sclerosis 1
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV004413226.1
First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024 |
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Likely benign
(May 07, 2021)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002614602.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of … (more)
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (less)
|
Comment:
Germline Functional Evidence
| 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. |
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Citations for germline classification of this variant
Help| There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for this variant ...
HelpRecord last updated Sep 29, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.