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_001080394.4(SPIDR):c.1610C>T (p.Ser537Leu)
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)
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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
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001080394.4(SPIDR):c.1610C>T (p.Ser537Leu)
Variation ID: 2596712 Accession: VCV002596712.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 8q11.21 8: 47673866 (GRCh38) [ NCBI UCSC ] 8: 48586428 (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 Oct 28, 2023 May 1, 2024 Jul 25, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001080394.4:c.1610C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001073863.1:p.Ser537Leu missense NM_001282916.1:c.1400C>T NP_001269845.1:p.Ser467Leu missense NM_001282919.1:c.1430C>T NP_001269848.1:p.Ser477Leu missense NM_001352931.1:c.1610C>T NP_001339860.1:p.Ser537Leu missense NM_001352932.1:c.1490C>T NP_001339861.1:p.Ser497Leu missense NM_001352933.1:c.1430C>T NP_001339862.1:p.Ser477Leu missense NM_001352934.1:c.1610C>T NP_001339863.1:p.Ser537Leu missense NM_001352935.1:c.1400C>T NP_001339864.1:p.Ser467Leu missense NM_001352936.1:c.1400C>T NP_001339865.1:p.Ser467Leu missense NM_001352937.1:c.1430C>T NP_001339866.1:p.Ser477Leu missense NM_001352938.1:c.1118C>T NP_001339867.1:p.Ser373Leu missense NM_001352939.1:c.1118C>T NP_001339868.1:p.Ser373Leu missense NM_001352940.1:c.1118C>T NP_001339869.1:p.Ser373Leu missense NM_001352941.1:c.1094C>T NP_001339870.1:p.Ser365Leu missense NM_001352942.1:c.953C>T NP_001339871.1:p.Ser318Leu missense NM_001352943.1:c.1118C>T NP_001339872.1:p.Ser373Leu missense NM_001352944.1:c.1094C>T NP_001339873.1:p.Ser365Leu missense NM_001352945.1:c.884C>T NP_001339874.1:p.Ser295Leu missense NM_001352946.1:c.860C>T NP_001339875.1:p.Ser287Leu missense NM_001352947.1:c.860C>T NP_001339876.1:p.Ser287Leu missense NM_001352948.1:c.860C>T NP_001339877.1:p.Ser287Leu missense NM_001352949.1:c.953C>T NP_001339878.1:p.Ser318Leu missense NM_001352950.1:c.1118C>T NP_001339879.1:p.Ser373Leu missense NM_001352951.1:c.860C>T NP_001339880.1:p.Ser287Leu missense NM_001352952.1:c.677C>T NP_001339881.1:p.Ser226Leu missense NM_001352953.1:c.677C>T NP_001339882.1:p.Ser226Leu missense NM_001352955.1:c.677C>T NP_001339884.1:p.Ser226Leu missense NM_001352956.1:c.677C>T NP_001339885.1:p.Ser226Leu missense NM_001352957.1:c.677C>T NP_001339886.1:p.Ser226Leu missense NM_001352958.1:c.362C>T NP_001339887.1:p.Ser121Leu missense NM_001352959.1:c.125C>T NP_001339888.1:p.Ser42Leu missense NM_001352960.1:c.35C>T NP_001339889.1:p.Ser12Leu missense NM_001352961.1:c.1610C>T NP_001339890.1:p.Ser537Leu missense NR_104581.1:n.1088C>T non-coding transcript variant NR_148202.1:n.1813C>T non-coding transcript variant NR_148203.1:n.1654C>T non-coding transcript variant NR_148204.1:n.1691C>T non-coding transcript variant NR_148205.1:n.1691C>T non-coding transcript variant NC_000008.11:g.47673866C>T NC_000008.10:g.48586428C>T - Protein change
- S318L, S467L, S121L, S295L, S365L, S12L, S42L, S226L, S287L, S373L, S477L, S497L, S537L
- Other names
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- Canonical SPDI
- NC_000008.11:47673865:C:T
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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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| SPIDR | - | - |
GRCh38 GRCh37 |
84 | 138 | |
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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Jul 25, 2023 | RCV004342684.1 |
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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Likely benign
(Jul 25, 2023)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV004065757.2
First in ClinVar: Oct 28, 2023 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 Nov 25, 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.