10-86917235-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_004329.3(BMPR1A):c.777G>A(p.Ala259Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000953 in 1,613,860 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A259A) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0020 ( 3 hom., cov: 32)

Exomes 𝑓: 0.00085 ( 14 hom. )

Consequence

BMPR1A
NM_004329.3 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:20

Conservation

PhyloP100: -0.625

Publications

5 publications found

Variant links:

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]

BMPR1A Gene-Disease associations (from GenCC):

generalized juvenile polyposis/juvenile polyposis coli
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, Genomics England PanelApp
juvenile polyposis syndrome
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P
polyposis syndrome, hereditary mixed, 2
Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
hereditary mixed polyposis syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
congenital heart defects, multiple types
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
pulmonary arterial hypertension
Inheritance: Unknown Classification: NO_KNOWN Submitted by: ClinGen

BMPR1A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 10-86917235-G-A is Benign according to our data. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-86917235-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136524.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.625 with no splicing effect.

BS1

Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00198 (301/152242) while in subpopulation EAS AF = 0.00984 (51/5182). AF 95% confidence interval is 0.00769. There are 3 homozygotes in GnomAd4. There are 147 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High AC in GnomAd4 at 301 AD,Unknown gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BMPR1A	NM_004329.3 link	c.777G>A	p.Ala259Ala	synonymous_variant	Exon 9 of 13	ENST00000372037.8	NP_004320.2	P36894

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BMPR1A	ENST00000372037.8 link	c.777G>A	p.Ala259Ala	synonymous_variant	Exon 9 of 13	1	NM_004329.3	ENSP00000361107.2		P36894

Frequencies

GnomAD3 genomes

AF:

0.00198

AC:

301

AN:

152124

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00522

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000197

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.0100

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.000848

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000191

Gnomad OTH

AF:

0.000958

GnomAD2 exomes

AF:

0.000851

AC:

213

AN:

250416

AF XY:

0.000701

show subpopulations

Gnomad AFR exome

AF:

0.00416

Gnomad AMR exome

AF:

0.000232

Gnomad ASJ exome

AF:

0.0000994

Gnomad EAS exome

AF:

0.00447

Gnomad FIN exome

AF:

0.000650

Gnomad NFE exome

AF:

0.000247

Gnomad OTH exome

AF:

0.000656

GnomAD4 exome

AF:

0.000846

AC:

1237

AN:

1461618

Hom.:

Cov.:

AF XY:

0.000828

AC XY:

602

AN XY:

727102

show subpopulations

African (AFR)

AF:

0.00514

AC:

172

AN:

33478

American (AMR)

AF:

0.000112

AC:

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.000153

AC:

AN:

26136

East Asian (EAS)

AF:

0.0197

AC:

780

AN:

39692

South Asian (SAS)

AF:

0.000244

AC:

AN:

86238

European-Finnish (FIN)

AF:

0.000656

AC:

AN:

53356

Middle Eastern (MID)

AF:

0.00139

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.000147

AC:

163

AN:

1111864

Other (OTH)

AF:

0.000812

AC:

AN:

60366

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

149

224

298

373

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00198

AC:

301

AN:

152242

Hom.:

Cov.:

AF XY:

0.00198

AC XY:

147

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.00522

AC:

217

AN:

41532

American (AMR)

AF:

0.000196

AC:

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.000288

AC:

AN:

3472

East Asian (EAS)

AF:

0.00984

AC:

AN:

5182

South Asian (SAS)

AF:

0.00104

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.000848

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000191

AC:

AN:

68018

Other (OTH)

AF:

0.000948

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000888

Hom.:

Bravo

AF:

0.00201

EpiCase

AF:

0.000218

EpiControl

AF:

0.0000593

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:20

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:7

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Mar 19, 2021

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Apr 21, 2014

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Nov 30, 2021

Genetic Services Laboratory, University of Chicago

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jan 06, 2017

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Sep 09, 2018

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Feb 16, 2025

Laboratory of Genetics, Children's Clinical University Hospital Latvia

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Hereditary cancer-predisposing syndrome

Benign:4

Apr 27, 2018

True Health Diagnostics

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Mar 21, 2016

Color Diagnostics, LLC DBA Color Health

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Feb 17, 2021

Sema4, Sema4

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:curation

- -

Oct 06, 2014

Ambry Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Juvenile polyposis syndrome

Benign:4

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jul 07, 2023

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Aug 05, 2024

Myriad Genetics, Inc.

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing. -

Feb 05, 2024

All of Us Research Program, National Institutes of Health

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:3

May 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

BMPR1A: BP4, BP7, BS1, BS2 -

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Jul 01, 2016

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant summary: The BMPR1A c.777G>A (p.Ala259Ala) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant while 4/5 splice tools predict the variant not to have an impact on normal splicing. This variant was found in 113/120202 control chromosomes at a frequency of 0.0009401, which is approximately 470 times the estimated maximal expected allele frequency of a pathogenic BMPR1A variant (0.000002), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as Benign/Likely Benign. Taken together, this variant is classified as Benign. -

Generalized juvenile polyposis/juvenile polyposis coli

Benign:1

Oct 29, 2018

Illumina Laboratory Services, Illumina

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

Juvenile polyposis syndrome;C1864730:Polyposis syndrome, hereditary mixed, 2

Benign:1

Nov 13, 2023

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

1.8

(source)

DANN

Benign

0.73

PhyloP100

-0.63

Mutation Taster

=99/1

polymorphism

(source)

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over