rs12477602

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001204.7(BMPR2):​c.418+5833G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,138 control chromosomes in the GnomAD database, including 1,193 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.12 ( 1193 hom., cov: 33)

Consequence

BMPR2
NM_001204.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.700
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BMPR2NM_001204.7 linkuse as main transcriptc.418+5833G>A intron_variant ENST00000374580.10
BMPR2XM_011511687.2 linkuse as main transcriptc.418+5833G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BMPR2ENST00000374580.10 linkuse as main transcriptc.418+5833G>A intron_variant 1 NM_001204.7 P1Q13873-1
BMPR2ENST00000374574.2 linkuse as main transcriptc.418+5833G>A intron_variant 2 Q13873-2
BMPR2ENST00000479069.1 linkuse as main transcriptn.326-1186G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.119
AC:
18084
AN:
152020
Hom.:
1190
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0907
Gnomad AMI
AF:
0.0768
Gnomad AMR
AF:
0.136
Gnomad ASJ
AF:
0.0692
Gnomad EAS
AF:
0.00385
Gnomad SAS
AF:
0.113
Gnomad FIN
AF:
0.189
Gnomad MID
AF:
0.0665
Gnomad NFE
AF:
0.135
Gnomad OTH
AF:
0.0899
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.119
AC:
18101
AN:
152138
Hom.:
1193
Cov.:
33
AF XY:
0.120
AC XY:
8951
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.0907
Gnomad4 AMR
AF:
0.136
Gnomad4 ASJ
AF:
0.0692
Gnomad4 EAS
AF:
0.00405
Gnomad4 SAS
AF:
0.114
Gnomad4 FIN
AF:
0.189
Gnomad4 NFE
AF:
0.135
Gnomad4 OTH
AF:
0.0889
Alfa
AF:
0.0644
Hom.:
79
Bravo
AF:
0.112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
2.4
DANN
Benign
0.47

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12477602; hg19: chr2-203338245; API