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NM_001079866.2(BCS1L):c.889+1G>T

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3
First in ClinVar:
Jan 6, 2017
Most recent Submission:
Mar 28, 2022
Last evaluated:
Aug 12, 2021
Accession:
VCV000370247.5
Variation ID:
370247
Description:
single nucleotide variant
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NM_001079866.2(BCS1L):c.889+1G>T

Allele ID
357243
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q35
Genomic location
2: 218662680 (GRCh38) GRCh38 UCSC
2: 219527403 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_001079866.2:c.889+1G>T MANE Select splice donor
NM_001257342.2:c.889+1G>T splice donor
NM_001257343.2:c.889+1G>T splice donor
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:218662679:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00001
Links
ClinGen: CA16040864
dbSNP: rs1057516346
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Aug 12, 2021 RCV000522697.4
Likely pathogenic 1 criteria provided, single submitter Dec 27, 2015 RCV000411192.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
BCS1L - - GRCh38
GRCh37
294 323

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Likely pathogenic
(Dec 27, 2015)
criteria provided, single submitter
Method: clinical testing
GRACILE syndrome
Affected status: unknown
Allele origin: unknown
Counsyl
Accession: SCV000485504.1
First in ClinVar: Jan 06, 2017
Last updated: Jan 06, 2017
Pathogenic
(Aug 14, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Affected status: yes
Allele origin: germline
GeneDx
Accession: SCV000619524.1
First in ClinVar: Dec 19, 2017
Last updated: Dec 19, 2017
Comment:
The c.889+1 G>T splice site variant in the BCS1L gene destroys the canonical splice donor site in intron 7. It is predicted to cause abnormal … (more)
Likely pathogenic
(Aug 12, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV002117415.1
First in ClinVar: Mar 28, 2022
Last updated: Mar 28, 2022

Functional evidence

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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 this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs1057516346...

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These 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 Aug 24, 2022