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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
ClinVar Genomic variation as it relates to human health
NM_014989.7(RIMS1):c.2865T>C (p.Ser955=)
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.
(1)
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.
Uncertain significance
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_014989.7(RIMS1):c.2865T>C (p.Ser955=)
Variation ID: 909160 Accession: VCV000909160.4
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 6q13 6: 72258219 (GRCh38) [ NCBI UCSC ] 6: 72967922 (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 May 31, 2020 May 31, 2020 Jan 13, 2018 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_014989.7:c.2865T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_055804.2:p.Ser955= synonymous NM_001168407.2:c.1284T>C NP_001161879.1:p.Ser428= synonymous NM_001168408.2:c.1287T>C NP_001161880.1:p.Ser429= synonymous NM_001168409.2:c.1044T>C NP_001161881.1:p.Ser348= synonymous NM_001168410.2:c.1242T>C NP_001161882.1:p.Ser414= synonymous NM_001350414.2:c.1287T>C NP_001337343.1:p.Ser429= synonymous NM_001350415.2:c.1284T>C NP_001337344.1:p.Ser428= synonymous NM_001350416.2:c.1287T>C NP_001337345.1:p.Ser429= synonymous NM_001350417.2:c.1287T>C NP_001337346.1:p.Ser429= synonymous NM_001350418.2:c.1284T>C NP_001337347.1:p.Ser428= synonymous NM_001350419.2:c.1284T>C NP_001337348.1:p.Ser428= synonymous NM_001350420.2:c.1287T>C NP_001337349.1:p.Ser429= synonymous NM_001350421.2:c.1215T>C NP_001337350.1:p.Ser405= synonymous NM_001350422.2:c.1284T>C NP_001337351.1:p.Ser428= synonymous NM_001350423.2:c.1284T>C NP_001337352.1:p.Ser428= synonymous NM_001350424.2:c.1218T>C NP_001337353.1:p.Ser406= synonymous NM_001350425.2:c.1284T>C NP_001337354.1:p.Ser428= synonymous NM_001350426.2:c.1287T>C NP_001337355.1:p.Ser429= synonymous NM_001350427.2:c.1284T>C NP_001337356.1:p.Ser428= synonymous NM_001350428.2:c.1218T>C NP_001337357.1:p.Ser406= synonymous NM_001350429.2:c.1287T>C NP_001337358.1:p.Ser429= synonymous NM_001350430.2:c.1215T>C NP_001337359.1:p.Ser405= synonymous NM_001350431.2:c.1287T>C NP_001337360.1:p.Ser429= synonymous NM_001350432.2:c.1284T>C NP_001337361.1:p.Ser428= synonymous NM_001350433.2:c.1287T>C NP_001337362.1:p.Ser429= synonymous NM_001350434.2:c.1284T>C NP_001337363.1:p.Ser428= synonymous NM_001350435.2:c.1284T>C NP_001337364.1:p.Ser428= synonymous NM_001350436.2:c.1284T>C NP_001337365.1:p.Ser428= synonymous NM_001350437.2:c.1215T>C NP_001337366.1:p.Ser405= synonymous NM_001350438.2:c.1284T>C NP_001337367.1:p.Ser428= synonymous NM_001350439.2:c.1287T>C NP_001337368.1:p.Ser429= synonymous NM_001350440.2:c.1284T>C NP_001337369.1:p.Ser428= synonymous NM_001350441.2:c.1284T>C NP_001337370.1:p.Ser428= synonymous NM_001350442.2:c.1287T>C NP_001337371.1:p.Ser429= synonymous NM_001350443.2:c.1284T>C NP_001337372.1:p.Ser428= synonymous NM_001350444.2:c.1284T>C NP_001337373.1:p.Ser428= synonymous NM_001350445.2:c.1284T>C NP_001337374.1:p.Ser428= synonymous NM_001350446.2:c.1287T>C NP_001337375.1:p.Ser429= synonymous NM_001350447.2:c.1284T>C NP_001337376.1:p.Ser428= synonymous NM_001350448.2:c.1287T>C NP_001337377.1:p.Ser429= synonymous NM_001350449.2:c.1284T>C NP_001337378.1:p.Ser428= synonymous NM_001350450.2:c.1215T>C NP_001337379.1:p.Ser405= synonymous NM_001350452.2:c.1287T>C NP_001337381.1:p.Ser429= synonymous NM_001350454.2:c.1284T>C NP_001337383.1:p.Ser428= synonymous NM_001350455.2:c.1287T>C NP_001337384.1:p.Ser429= synonymous NM_001350456.2:c.1284T>C NP_001337385.1:p.Ser428= synonymous NM_001350457.2:c.1287T>C NP_001337386.1:p.Ser429= synonymous NM_001350458.2:c.1287T>C NP_001337387.1:p.Ser429= synonymous NM_001350459.2:c.1218T>C NP_001337388.1:p.Ser406= synonymous NM_001350460.2:c.1287T>C NP_001337389.1:p.Ser429= synonymous NM_001350461.2:c.1041T>C NP_001337390.1:p.Ser347= synonymous NM_001350462.2:c.1218T>C NP_001337391.1:p.Ser406= synonymous NM_001350463.2:c.1041T>C NP_001337392.1:p.Ser347= synonymous NM_001350464.2:c.1044T>C NP_001337393.1:p.Ser348= synonymous NM_001350465.2:c.1044T>C NP_001337394.1:p.Ser348= synonymous NM_001350466.2:c.1044T>C NP_001337395.1:p.Ser348= synonymous NM_001350467.2:c.1044T>C NP_001337396.1:p.Ser348= synonymous NM_001350468.2:c.1041T>C NP_001337397.1:p.Ser347= synonymous NM_001350469.2:c.1044T>C NP_001337398.1:p.Ser348= synonymous NM_001350470.2:c.1242T>C NP_001337399.1:p.Ser414= synonymous NM_001350471.2:c.1215T>C NP_001337400.1:p.Ser405= synonymous NM_001350472.2:c.1239T>C NP_001337401.1:p.Ser413= synonymous NM_001350473.2:c.1242T>C NP_001337402.1:p.Ser414= synonymous NM_001350474.2:c.1242T>C NP_001337403.1:p.Ser414= synonymous NC_000006.12:g.72258219T>C NC_000006.11:g.72967922T>C NG_016209.1:g.376273T>C - Protein change
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- Other names
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- Canonical SPDI
- NC_000006.12:72258218:T:C
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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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Trans-Omics for Precision Medicine (TOPMed) 0.00000
The Genome Aggregation Database (gnomAD) 0.00001
- 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. |
|||
| RIMS1 | Little evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
1141 | 1188 | |
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. |
|---|---|---|---|---|
| Uncertain significance (1) |
criteria provided, single submitter
|
Jan 13, 2018 | RCV001160103.4 |
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. |
|
|---|---|---|---|---|---|
|
Uncertain significance
(Jan 13, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Cone-rod dystrophy 7
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV001321873.1
First in ClinVar: May 31, 2020 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. (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 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
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 rs2076658233 ...
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 Jul 08, 2023
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.