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NM_004329.3(BMPR1A):c.1560G>A (p.Thr520=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Mar 31, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000136527.8
Variation ID:
136527
Description:
single nucleotide variant
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NM_004329.3(BMPR1A):c.1560G>A (p.Thr520=)

Allele ID
140230
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q23.2
Genomic location
10: 86923680 (GRCh38) GRCh38 UCSC
10: 88683437 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_298:g.172042G>A
LRG_298t1:c.1560G>A LRG_298p1:p.Thr520=
NC_000010.10:g.88683437G>A
... more HGVS
Protein change
-
Other names
p.T520T:ACG>ACA
Canonical SPDI
NC_000010.11:86923679:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00035
1000 Genomes Project 0.00040
The Genome Aggregation Database (gnomAD) 0.00096
Trans-Omics for Precision Medicine (TOPMed) 0.00126
The Genome Aggregation Database (gnomAD) 0.00136
Trans-Omics for Precision Medicine (TOPMed) 0.00136
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00146
The Genome Aggregation Database (gnomAD), exomes 0.00031
Links
ClinGen: CA201034
dbSNP: rs142775086
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 Mar 9, 2016 RCV000123861.7
Benign 4 criteria provided, multiple submitters, no conflicts Jul 13, 2017 RCV000174534.4
Benign 1 criteria provided, single submitter Jul 13, 2017 RCV000759480.4
Benign 1 criteria provided, single submitter Dec 8, 2020 RCV001079281.2
Likely benign 1 no assertion criteria provided - RCV001356619.1
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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
(Feb 26, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000167204.11
Submitted: (Mar 26, 2018)
Evidence details
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)
Benign
(Apr 25, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000225849.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Oct 30, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000213642.5
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, … (more)
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Juvenile polyposis syndrome
Allele origin: germline
Invitae
Accession: SCV000261826.8
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jul 13, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000600221.1
Submitted: (Aug 01, 2017)
Evidence details
Benign
(Mar 09, 2016)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000682877.1
Submitted: (Oct 26, 2017)
Evidence details
Benign
(Jul 13, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000888822.1
Submitted: (Aug 31, 2018)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000691805.1
Submitted: (Oct 31, 2017)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
Carcinoma of colon
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: SCV001551837.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
The BMPR1A p.Thr520= variant was not identified in the literature nor was it identified in the Cosmic or LOVD 3.0 databases. The variant was identified … (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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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=BMPR1A - - - -

Text-mined citations for rs142775086...

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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