2-202376511-A-AGGCGGCGGC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001204.7(BMPR2):c.-936_-928dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.074 (457 hom., cov: 16)
• Consequence: BMPR2 NM_001204.7 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.67

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 -10 ACMG points.

• BP6: Variant 2-202376511-A-AGGCGGCGGC is Benign according to our data. Variant chr2-202376511-A-AGGCGGCGGC is described in ClinVar as [Benign]. Clinvar id is 1238911.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BMPR2	NM_001204.7	c.-936_-928dup		5_prime_UTR_variant	1/13	ENST00000374580.10
BMPR2	XM_011511687.2	c.-936_-928dup		5_prime_UTR_variant	1/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BMPR2	ENST00000374580.10	c.-936_-928dup		5_prime_UTR_variant	1/13	1	NM_001204.7	P1

Frequencies

GnomAD3 genomes AF: 0.0736 AC: 9247 AN: 125682 Hom.: 456 Cov.: 16

Gnomad AFR AF: 0.0428

Gnomad AMI AF: 0.0468

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.00382

Gnomad SAS AF: 0.0591

Gnomad FIN AF: 0.0746

Gnomad MID AF: 0.0551

Gnomad NFE AF: 0.0944

Gnomad OTH AF: 0.0488

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

GnomAD4 genome AF: 0.0736 AC: 9256 AN: 125786 Hom.: 457 Cov.: 16 AF XY: 0.0710 AC XY: 4274 AN XY: 60200

Gnomad4 AFR AF: 0.0428

Gnomad4 AMR AF: 0.0912

Gnomad4 ASJ AF: 0.0741

Gnomad4 EAS AF: 0.00383

Gnomad4 SAS AF: 0.0595

Gnomad4 FIN AF: 0.0746

Gnomad4 NFE AF: 0.0944

Gnomad4 OTH AF: 0.0483

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 10, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs375624016; hg19: chr2-203241234;