GeneBe

rs375624016

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001204.7(BMPR2):​c.-954_-928delGGCGGCGGCGGCGGCGGCGGCGGCGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000080 ( 0 hom., cov: 16)

Consequence

BMPR2
NM_001204.7 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.43
Variant links:
Genes affected
BMPR2 (HGNC:1078): (bone morphogenetic protein receptor type 2) This gene encodes a member of the bone morphogenetic protein (BMP) receptor family of transmembrane serine/threonine kinases. The ligands of this receptor are members of the TGF-beta superfamily. BMPs are involved in endochondral bone formation and embryogenesis. These proteins transduce their signals through the formation of heteromeric complexes of two different types of serine (threonine) kinase receptors: type I receptors of about 50-55 kD and type II receptors of about 70-80 kD. Mutations in this gene have been associated with primary pulmonary hypertension, both familial and fenfluramine-associated, and with pulmonary venoocclusive disease. [provided by RefSeq, May 2020]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BMPR2NM_001204.7 linkc.-954_-928delGGCGGCGGCGGCGGCGGCGGCGGCGGC 5_prime_UTR_variant Exon 1 of 13 ENST00000374580.10 NP_001195.2 Q13873-1
BMPR2XM_011511687.2 linkc.-954_-928delGGCGGCGGCGGCGGCGGCGGCGGCGGC 5_prime_UTR_variant Exon 1 of 13 XP_011509989.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BMPR2ENST00000374580.10 linkc.-954_-928delGGCGGCGGCGGCGGCGGCGGCGGCGGC 5_prime_UTR_variant Exon 1 of 13 1 NM_001204.7 ENSP00000363708.4 Q13873-1
ENSG00000273456ENST00000724884.1 linkn.154+253_154+279delGCCGCCGCCGCCGCCGCCGCCGCCGCC intron_variant Intron 1 of 1
ENSG00000273456ENST00000724885.1 linkn.106+95_106+121delGCCGCCGCCGCCGCCGCCGCCGCCGCC intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.00000795
AC:
1
AN:
125760
Hom.:
0
Cov.:
16
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000170
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00000795
AC:
1
AN:
125760
Hom.:
0
Cov.:
16
AF XY:
0.0000166
AC XY:
1
AN XY:
60126
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33904
American (AMR)
AF:
0.00
AC:
0
AN:
11806
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3186
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4188
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2946
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
8248
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
272
European-Non Finnish (NFE)
AF:
0.0000170
AC:
1
AN:
58928
Other (OTH)
AF:
0.00
AC:
0
AN:
1556
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs375624016; hg19: chr2-203241234; API