2-202420434-T-G

Variant names:

• chr2-202420434-T-G
• rs6747299
• NM_001204.7:c.76+42884T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001204.7(BMPR2):​c.76+42884T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,794 control chromosomes in the GnomAD database, including 19,772 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 0.50 (19772 hom., cov: 32)
• Consequence: BMPR2 NM_001204.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BMPR2	NM_001204.7	c.76+42884T>G		intron_variant	Intron 1 of 12	ENST00000374580.10	NP_001195.2
BMPR2	XM_011511687.2	c.76+42884T>G		intron_variant	Intron 1 of 12		XP_011509989.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BMPR2	ENST00000374580.10	c.76+42884T>G		intron_variant	Intron 1 of 12	1	NM_001204.7	ENSP00000363708.4
BMPR2	ENST00000374574.2	c.76+42884T>G		intron_variant	Intron 1 of 11	2		ENSP00000363702.2

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76226 AN: 151676 Hom.: 19741 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.503 AC: 76309 AN: 151794 Hom.: 19772 Cov.: 32 AF XY: 0.497 AC XY: 36880 AN XY: 74180

African (AFR) AF: 0.611 AC: 25321 AN: 41422

American (AMR) AF: 0.486 AC: 7385 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1265 AN: 3466

East Asian (EAS) AF: 0.176 AC: 912 AN: 5170

South Asian (SAS) AF: 0.461 AC: 2220 AN: 4820

European-Finnish (FIN) AF: 0.447 AC: 4677 AN: 10468

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.483 AC: 32786 AN: 67926

Other (OTH) AF: 0.513 AC: 1082 AN: 2110

Alfa AF: 0.488 Hom.: 10646

Bravo AF: 0.511

Asia WGS AF: 0.360 AC: 1252 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.41
PhyloP100		-0.59
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

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Other links and lift over

dbSNP: rs6747299; hg19: chr2-203285157;