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NM_004329.3(BMPR1A):c.676-5T>C

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Sep 17, 2021)
Last evaluated:
Dec 1, 2020
Accession:
VCV000136052.11
Variation ID:
136052
Description:
single nucleotide variant
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NM_004329.3(BMPR1A):c.676-5T>C

Allele ID
139764
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q23.2
Genomic location
10: 86917129 (GRCh38) GRCh38 UCSC
10: 88676886 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_298:g.165491T>C
LRG_298t1:c.676-5T>C
NC_000010.11:g.86917129T>C
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000010.11:86917128:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00599 (C)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00003
The Genome Aggregation Database (gnomAD) 0.00006
The Genome Aggregation Database (gnomAD), exomes 0.00222
Trans-Omics for Precision Medicine (TOPMed) 0.00013
1000 Genomes Project 0.00599
Exome Aggregation Consortium (ExAC) 0.00259
The Genome Aggregation Database (gnomAD) 0.00001
Links
ClinGen: CA169033
dbSNP: rs200537780
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Feb 4, 2019 RCV000131998.6
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000123226.12
Benign 1 criteria provided, single submitter Dec 1, 2020 RCV001507250.1
Benign 1 criteria provided, single submitter Mar 3, 2015 RCV001668280.2
Likely benign 1 no assertion criteria provided - RCV000582818.1
Benign 1 no assertion criteria provided - RCV001354511.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
BMPR1A Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1401 1452

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Generalized juvenile polyposis/juvenile polyposis coli
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000365648.3
Submitted: (Feb 20, 2020)
Evidence details
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)
Likely benign
(Feb 04, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000187057.6
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Subpopulation frequency in support of benign classification
Benign
(Dec 01, 2020)
criteria provided, single submitter
Method: clinical testing
Juvenile polyposis syndrome
Allele origin: germline
Invitae
Accession: SCV000166532.11
Submitted: (Jan 07, 2021)
Evidence details
Benign
(May 16, 2016)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000910562.1
Submitted: (Nov 06, 2018)
Evidence details
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001890858.1
Submitted: (Sep 17, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000691801.1
Submitted: (Oct 31, 2017)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
Hereditary mixed polyposis syndrome 2
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001549148.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The BMPR1A c.676-5T>C variant was not identified in the literature nor was it identified in the LOVD 3.0 database. The variant was identified in dbSNP … (more)

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 rs200537780...

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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 Nov 27, 2021