10-86758367-ATT-A

Variant summary

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

The NM_004329.3(BMPR1A):c.-268+1464_-268+1465del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.29 (6164 hom., cov: 0)
• Consequence: BMPR1A NM_004329.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0790

Genes affected

BMPR1A (HGNC:1076): (bone morphogenetic protein receptor type 1A) The bone morphogenetic protein (BMP) receptors are a family of transmembrane serine/threonine kinases that include the type I receptors BMPR1A and BMPR1B and the type II receptor BMPR2. These receptors are also closely related to the activin receptors, ACVR1 and ACVR2. The ligands of these receptors are members of the TGF-beta superfamily. TGF-betas and activins transduce their signals through the formation of heteromeric complexes with 2 different types of serine (threonine) kinase receptors: type I receptors of about 50-55 kD and type II receptors of about 70-80 kD. Type II receptors bind ligands in the absence of type I receptors, but they require their respective type I receptors for signaling, whereas type I receptors require their respective type II receptors for ligand binding. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 10-86758367-ATT-A is Benign according to our data. Variant chr10-86758367-ATT-A is described in ClinVar as [Benign]. Clinvar id is 1226909.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BMPR1A	NM_004329.3	c.-268+1464_-268+1465del		intron_variant		ENST00000372037.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BMPR1A	ENST00000372037.8	c.-268+1464_-268+1465del		intron_variant		1	NM_004329.3	P1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 41171 AN: 140864 Hom.: 6165 Cov.: 0

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.292 AC: 41183 AN: 140906 Hom.: 6164 Cov.: 0 AF XY: 0.300 AC XY: 20389 AN XY: 67976

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.293

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

May 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs200528013; hg19: chr10-88518124;