NM_001204.7(BMPR2):c.-669G>A AND Primary pulmonary hypertension

Germline classification:: Benign (2 submissions)
Last evaluated:: Apr 14, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001516961.15

Allele description [Variation Report for NM_001204.7(BMPR2):c.-669G>A]

NM_001204.7(BMPR2):c.-669G>A

Genes:

LOC129935434:ATAC-STARR-seq lymphoblastoid silent region 12244 [Gene]
BMPR2:bone morphogenetic protein receptor type 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q33.1

Genomic location:

Preferred name:

NM_001204.7(BMPR2):c.-669G>A

HGVS:

NC_000002.12:g.202376806G>A
NG_009363.1:g.5480G>A
NM_001204.7:c.-669G>AMANE SELECT
LRG_712t1:c.-669G>A
LRG_712:g.5480G>A
NC_000002.11:g.203241529G>A
NM_001204.6:c.-669G>A

Links:

dbSNP: rs115604088

NCBI 1000 Genomes Browser:

rs115604088

Molecular consequence:

NM_001204.7:c.-669G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Name:: Primary pulmonary hypertension (PPH1)
Identifiers:: MONDO: MONDO:0001999; MedGen: C0152171

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Variola albimarginata voucher FDP_IGCS_2111_013A cytochrome oxidase subunit 1 (C...
Variola albimarginata voucher FDP_IGCS_2111_013A cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial
gi|2722342358|gnl|uoguelph|MINDA202 OI-5P|gb|OR524716.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000575939	Rare Disease Genomics Group, St George's University of London	no assertion criteria provided	Benign (Feb 7, 2024)	germline	literature only
SCV001725339	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Apr 14, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000575939

Rare Disease Genomics Group, St George's University of London

no assertion criteria provided

Benign
(Feb 7, 2024)

germline

literature only

SCV001725339

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Apr 14, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Rare Disease Genomics Group, St George's University of London, SCV000575939.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	not provided

Description

The NM_001204.7(BMPR2):c.-669G>A variant has an allele frequency of >2% in the European (Finnish) population and has been observed in the homozygous state (n=24) in the gnomAD database (v.4.0.0). Therefore, this variant meets our criteria to be classified as benign, based on allele frequency data.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001725339.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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