rs13010656

chr2-202432345-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001204.7(BMPR2):c.77-32464T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 150,198 control chromosomes in the GnomAD database, including 19,183 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 0.49 (19183 hom., cov: 32)
• Consequence: BMPR2 NM_001204.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BMPR2	NM_001204.7	c.77-32464T>G		intron_variant		ENST00000374580.10
BMPR2	XM_011511687.2	c.77-32464T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BMPR2	ENST00000374580.10	c.77-32464T>G		intron_variant		1	NM_001204.7	P1
BMPR2	ENST00000374574.2	c.77-32464T>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.486 AC: 72980 AN: 150078 Hom.: 19151 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.501

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.486 AC: 73063 AN: 150198 Hom.: 19183 Cov.: 32 AF XY: 0.481 AC XY: 35304 AN XY: 73398

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.502

Alfa AF: 0.491 Hom.: 2540

Bravo AF: 0.494

Asia WGS AF: 0.357 AC: 1234 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.11
Dann	Benign	0.53

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

Other links and lift over

dbSNP: rs13010656; hg19: chr2-203297068;