ClinVar Genomic variation as it relates to human health
NM_016729.3(FOLR1):c.493+2T>C
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.
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(5); Benign(5)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_016729.3(FOLR1):c.493+2T>C
Variation ID: 95750 Accession: VCV000095750.43
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 11q13.4 11: 72195749 (GRCh38) [ NCBI UCSC ] 11: 71906793 (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 Apr 4, 2013 Oct 20, 2024 Aug 1, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_016729.3:c.493+2T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
splice donor NM_000802.3:c.493+2T>C splice donor NM_016724.3:c.493+2T>C splice donor NM_016725.3:c.493+2T>C splice donor NC_000011.10:g.72195749T>C NC_000011.9:g.71906793T>C NC_000011.8:g.71584441T>C NG_015863.1:g.11192T>C - Protein change
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- Other names
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FOLR1, SPLICE SITE MUTATION
- Canonical SPDI
- NC_000011.10:72195748: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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0.00339 (C)
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Allele frequency
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The frequency of the allele represented by this VCV record.
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The Genome Aggregation Database (gnomAD) 0.00134
Trans-Omics for Precision Medicine (TOPMed) 0.00168
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00208
1000 Genomes Project 30x 0.00297
The Genome Aggregation Database (gnomAD), exomes 0.00338
1000 Genomes Project 0.00339
Exome Aggregation Consortium (ExAC) 0.00343
- 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 | ||
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HI score
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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
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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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FOLR1 | - | - |
GRCh38 GRCh37 |
260 | 274 |
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. |
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Conflicting interpretations of pathogenicity (5) |
criteria provided, conflicting classifications
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Aug 1, 2024 | RCV000081793.37 | |
Conflicting interpretations of pathogenicity (6) |
criteria provided, conflicting classifications
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Jan 30, 2024 | RCV000356764.40 | |
FOLR1-related disorder
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Likely benign (1) |
no assertion criteria provided
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May 1, 2019 | RCV003925073.2 |
Uncertain significance (1) |
no assertion criteria provided
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Aug 25, 2017 | RCV000781973.9 | |
Uncertain significance (1) |
criteria provided, single submitter
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Dec 6, 2019 | RCV002313796.9 |
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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Uncertain significance
(Nov 23, 2015)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000331322.4
First in ClinVar: Dec 06, 2016 Last updated: Jul 31, 2019 |
Number of individuals with the variant: 11
Sex: mixed
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Benign
(-)
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criteria provided, single submitter
Method: research
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Cerebral folate transport deficiency
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
Accession: SCV001435221.1
First in ClinVar: Oct 03, 2020 Last updated: Oct 03, 2020 |
Comment:
The homozygous c.493+2T>C variant in FOLR1 and has been identified in at least 1 individual with intellectual disability (PMID: 21937992), and has been identified in … (more)
The homozygous c.493+2T>C variant in FOLR1 and has been identified in at least 1 individual with intellectual disability (PMID: 21937992), and has been identified in >1% of South Asian chromosomes and 8 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as benign for autosomal recessive folate receptor deficiency. (less)
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Benign
(Jan 30, 2024)
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criteria provided, single submitter
Method: clinical testing
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Cerebral folate transport deficiency
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000648581.8
First in ClinVar: Dec 26, 2017 Last updated: Feb 20, 2024 |
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Uncertain Significance
(Sep 12, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV004848158.1
First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024 |
Comment:
The c.493+2T>C variant in FOLR1 has been reported in at least 3 individuals with neurologic disease (Najmabadi 2011 PMID: 21937992, McCreary 2019 PMID: 31664448, Hiz … (more)
The c.493+2T>C variant in FOLR1 has been reported in at least 3 individuals with neurologic disease (Najmabadi 2011 PMID: 21937992, McCreary 2019 PMID: 31664448, Hiz Kurul 2022 PMID: 34791078). It has also been identified in 1.4% (430/30614) of South Asian chromosomes by gnomAD including 8 homozygotes (http://gnomad.broadinstitute.org, v.2.1.2), which is higher than expected for a disease-causing variant in FOLR1. This variant has also been reported in ClinVar (Variation ID 95750). This variant occurs within the canonical splice site (+/- 1,2) of the last intron of the FOLR1 gene and is predicted to cause altered splicing. In summary, due to the conflicting evidence, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PVS1_Strong, BS1. (less)
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Uncertain significance
(Dec 06, 2019)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV000847409.5
First in ClinVar: Nov 08, 2018 Last updated: May 01, 2024 |
Comment:
The c.493+2T>C intronic variant results from a T to C substitution two nucleotides after coding exon 3 in the FOLR1 gene. Alterations that disrupt the … (more)
The c.493+2T>C intronic variant results from a T to C substitution two nucleotides after coding exon 3 in the FOLR1 gene. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. Using two different splice site prediction tools, this alteration is predicted by BDGP to abolish the native splice donor site, but is predicted to weaken (but not abolish) the efficiency of the native splice donor site by ESEfinder; however, direct evidence is unavailable. In one study, this alteration was detected as homozygous in three siblings from a consanguineous family with symptoms of cerebral folate transport deficiency (Najmabadi H et al. Nature, 2011 Oct;478:57-63). This variant occurred in the homozygous state in a reportedly healthy mother of three heterozygous daughters, one described as having clinical Rett syndrome, and two with autism and epilepsy (Ramaekers VT et al. Mol Genet Metab. 2018 May;124(1):87-93). Based on data from gnomAD, this variant has an overall frequency of approximately 0.31% (861/277102) and has been seen as homozygous in 10 individuals. The highest observed frequency was 1.4% (434/30780) in the South Asian subpopulation. Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear. (less)
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Benign
(Aug 01, 2024)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV004137226.10
First in ClinVar: Nov 20, 2023 Last updated: Oct 20, 2024 |
Comment:
FOLR1: BS1, BS2
Number of individuals with the variant: 7
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Uncertain significance
(Jul 05, 2017)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: not provided
Allele origin:
germline
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Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
Accession: SCV000280715.2
First in ClinVar: Aug 07, 2015 Last updated: Nov 04, 2017 |
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Uncertain significance
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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Cerebral folate transport deficiency
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV001268708.1
First in ClinVar: May 31, 2020 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. (less)
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Benign
(Jul 29, 2019)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000241008.10
First in ClinVar: Aug 07, 2015 Last updated: Mar 08, 2017 |
Comment:
This variant is associated with the following publications: (PMID: 31664448, 29961769, 29661558, 27535533, 27884173, 21937992)
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Benign
(-)
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criteria provided, single submitter
Method: clinical testing
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Cerebral folate transport deficiency
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV002820171.2
First in ClinVar: Jan 21, 2023 Last updated: May 01, 2024 |
Comment:
The splice donor variant c.493+2T>C in FOLR1 (NM_016725.3) has been reported previously as homozygous in three siblings from a consanguineous family with symptoms of cerebral … (more)
The splice donor variant c.493+2T>C in FOLR1 (NM_016725.3) has been reported previously as homozygous in three siblings from a consanguineous family with symptoms of cerebral folate transport deficiency (Najmabadi H et al, 2011). It has also been recently reported in trans with a pathogenic variant in an adult patient with stable clinical and MRI features.The c.493+2T>C variant is observed in 430/30,614 (1.4046%) alleles from individuals of South Asian background in gnomAD Exomes and in 13/978 (1.3292%) alleles from individuals of South Asian background in 1000 Genomes. It has been observed in homozygous state in gnomad database in multiple individuals. Considering the high frequency of the variant the possibility that it is disease causing is unlikely and hence the variant has been classified as Benign. (less)
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Uncertain significance
(Jun 07, 2017)
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no assertion criteria provided
Method: curation
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Cerebral folate transport deficiency
Affected status: no
Allele origin:
germline
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SingHealth Duke-NUS Institute of Precision Medicine
Accession: SCV000853162.1
First in ClinVar: Nov 25, 2018 Last updated: Nov 25, 2018 |
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Uncertain significance
(Aug 25, 2017)
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no assertion criteria provided
Method: clinical testing
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Seizures
Affected status: yes
Allele origin:
germline
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Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital
Accession: SCV000920428.1
First in ClinVar: Jun 03, 2019 Last updated: Jun 03, 2019 |
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Likely benign
(May 01, 2019)
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no assertion criteria provided
Method: clinical testing
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FOLR1-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004744864.2
First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024 |
Comment:
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
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Pathogenic
(Sep 21, 2011)
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Flagged submission
flagged submission
Method: literature only
Reason: Outlier claim with insufficient supporting evidence
Source: ClinGen
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FOLATE RECEPTOR DEFICIENCY
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000053287.1
First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013 |
Comment on evidence:
In a couple who were double second cousins and had 3 children affected with severe intellectual disability, ataxia, spastic paraplegia, hearing loss, and visual disturbances … (more)
In a couple who were double second cousins and had 3 children affected with severe intellectual disability, ataxia, spastic paraplegia, hearing loss, and visual disturbances (613068), Najmabadi et al. (2011) found a splice site mutation, a T-to-C transition at genomic coordinate 71584441, that was found in homozygosity in all affected individuals. Both parents were carriers. (less)
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Flagged submissions do not contribute to the aggregate classification or review status for the variant. Learn more |
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. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Population genomics in South East Asia captures unexpectedly high carrier frequency for treatable inherited disorders. | Bylstra Y | Genetics in medicine : official journal of the American College of Medical Genetics | 2019 | PMID: 29961769 |
Genetic assessment and folate receptor autoantibodies in infantile-onset cerebral folate deficiency (CFD) syndrome. | Ramaekers VT | Molecular genetics and metabolism | 2018 | PMID: 29661558 |
Revisiting the morbid genome of Mendelian disorders. | Abouelhoda M | Genome biology | 2016 | PMID: 27884173 |
Analysis of protein-coding genetic variation in 60,706 humans. | Lek M | Nature | 2016 | PMID: 27535533 |
Deep sequencing reveals 50 novel genes for recessive cognitive disorders. | Najmabadi H | Nature | 2011 | PMID: 21937992 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=FOLR1 | - | - | - | - |
Text-mined citations for rs144637717 ...
HelpRecord last updated Nov 03, 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.