ClinVar Genomic variation as it relates to human health
NM_001079866.2(BCS1L):c.613G>A (p.Val205Ile)
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(1); Benign(7); Likely benign(1)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001079866.2(BCS1L):c.613G>A (p.Val205Ile)
Variation ID: 214159 Accession: VCV000214159.31
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 2q35 2: 218661911 (GRCh38) [ NCBI UCSC ] 2: 219526634 (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 11, 2015 Mar 16, 2024 Jan 31, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001079866.2:c.613G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001073335.1:p.Val205Ile missense NM_001257342.2:c.613G>A NP_001244271.1:p.Val205Ile missense NM_001257343.2:c.613G>A NP_001244272.1:p.Val205Ile missense NM_001257344.2:c.613G>A NP_001244273.1:p.Val205Ile missense NM_001318836.2:c.253G>A NP_001305765.1:p.Val85Ile missense NM_001320717.2:c.613G>A NP_001307646.1:p.Val205Ile missense NM_001371443.1:c.613G>A NP_001358372.1:p.Val205Ile missense NM_001371444.1:c.613G>A NP_001358373.1:p.Val205Ile missense NM_001371446.1:c.613G>A NP_001358375.1:p.Val205Ile missense NM_001371447.1:c.613G>A NP_001358376.1:p.Val205Ile missense NM_001371448.1:c.613G>A NP_001358377.1:p.Val205Ile missense NM_001371449.1:c.613G>A NP_001358378.1:p.Val205Ile missense NM_001371450.1:c.613G>A NP_001358379.1:p.Val205Ile missense NM_001371451.1:c.253G>A NP_001358380.1:p.Val85Ile missense NM_001371452.1:c.112G>A NP_001358381.1:p.Val38Ile missense NM_001371453.1:c.112G>A NP_001358382.1:p.Val38Ile missense NM_001371454.1:c.112G>A NP_001358383.1:p.Val38Ile missense NM_001371455.1:c.112G>A NP_001358384.1:p.Val38Ile missense NM_001371456.1:c.112G>A NP_001358385.1:p.Val38Ile missense NM_001374085.1:c.613G>A NP_001361014.1:p.Val205Ile missense NM_001374086.1:c.112G>A NP_001361015.1:p.Val38Ile missense NM_004328.5:c.613G>A NP_004319.1:p.Val205Ile missense NR_163955.1:n.1625G>A non-coding transcript variant NC_000002.12:g.218661911G>A NC_000002.11:g.219526634G>A NG_008018.1:g.7256G>A NG_033099.1:g.2630C>T LRG_539:g.7256G>A LRG_539t1:c.613G>A LRG_539p1:p.Val205Ile - Protein change
- V205I, V85I, V38I
- Other names
- p.V205I:GTC>ATC
- Canonical SPDI
- NC_000002.12:218661910:G:A
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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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0.00619 (A)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
The Genome Aggregation Database (gnomAD) 0.00295
Exome Aggregation Consortium (ExAC) 0.00553
1000 Genomes Project 0.00619
Trans-Omics for Precision Medicine (TOPMed) 0.00620
1000 Genomes Project 30x 0.00703
The Genome Aggregation Database (gnomAD), exomes 0.00756
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
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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BCS1L | - | - |
GRCh38 GRCh37 |
484 | 519 |
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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Benign (2) |
criteria provided, multiple submitters, no conflicts
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Mar 21, 2016 | RCV000200623.15 | |
Likely benign (1) |
criteria provided, single submitter
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Aug 7, 2018 | RCV000714568.11 | |
Benign (2) |
criteria provided, multiple submitters, no conflicts
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Jan 31, 2024 | RCV000949252.23 | |
Benign (1) |
criteria provided, single submitter
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Apr 27, 2017 | RCV001137962.12 | |
Benign (2) |
criteria provided, single submitter
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Apr 27, 2017 | RCV001137963.13 | |
Uncertain significance (1) |
criteria provided, single submitter
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Apr 27, 2017 | RCV001137961.12 | |
Benign (1) |
criteria provided, single submitter
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Sep 25, 2019 | RCV003917794.1 |
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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Benign
(Jul 08, 2014)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000251192.11
First in ClinVar: Oct 11, 2015 Last updated: Apr 09, 2018 |
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. (less)
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Likely benign
(Aug 07, 2018)
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criteria provided, single submitter
Method: clinical testing
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BCS1L-Related Disorders
Affected status: yes
Allele origin:
inherited
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Genomic Research Center, Shahid Beheshti University of Medical Sciences
Accession: SCV000845270.1
First in ClinVar: Nov 03, 2018 Last updated: Nov 03, 2018 |
Number of individuals with the variant: 1
Sex: male
Geographic origin: Iran
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Benign
(Mar 21, 2016)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: not provided
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000711832.1
First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018 |
Comment:
p.Val205Ile in exon 5 of BCS1L: This variant is not expected to have clinical si gnificance because it has been identified in 5.64% (644/11418) of … (more)
p.Val205Ile in exon 5 of BCS1L: This variant is not expected to have clinical si gnificance because it has been identified in 5.64% (644/11418) of Latino chromos omes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs148278887). (less)
Number of individuals with the variant: 2
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Benign
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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GRACILE syndrome
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV001297963.1
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). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. (less)
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Uncertain significance
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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Mitochondrial complex III deficiency nuclear type 1
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV001297961.1
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). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. (less)
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Benign
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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Leigh syndrome
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV001297962.1
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). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. (less)
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Benign
(Jan 31, 2024)
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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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Invitae
Accession: SCV001095502.6
First in ClinVar: Dec 17, 2019 Last updated: Feb 20, 2024 |
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Benign
(Nov 28, 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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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000602631.6
First in ClinVar: Oct 11, 2015 Last updated: Feb 20, 2024 |
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Benign
(Sep 25, 2019)
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criteria provided, single submitter
Method: clinical testing
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BCS1L-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004736388.1
First in ClinVar: Mar 16, 2024 Last updated: Mar 16, 2024 |
Comment:
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
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Benign
(Sep 16, 2020)
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no assertion criteria provided
Method: clinical testing
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GRACILE syndrome
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV001455776.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
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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
HelpThere 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 rs148278887 ...
HelpRecord last updated Apr 15, 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.