Variant rs13037675 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001200.4(BMP2):c.1161C>T(p.Asp387=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0667 in 1,610,308 control chromosomes in the GnomAD database, including 4,191 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.064 ( 373 hom., cov: 31)

Exomes 𝑓: 0.067 ( 3818 hom. )

Consequence

BMP2
NM_001200.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 2.20

Variant links:

Genes affected

BMP2 (HGNC:1069): (bone morphogenetic protein 2) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer, which plays a role in bone and cartilage development. Duplication of a regulatory region downstream of this gene causes a form of brachydactyly characterized by a malformed index finger and second toe in human patients. [provided by RefSeq, Jul 2016]

BMP2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 20-6779059-C-T is Benign according to our data. Variant chr20-6779059-C-T is described in ClinVar as [Benign]. Clinvar id is 257620.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.2 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BMP2	NM_001200.4 linkuse as main transcript	c.1161C>T	p.Asp387=	synonymous_variant	3/3	ENST00000378827.5	NP_001191.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BMP2	ENST00000378827.5 linkuse as main transcript	c.1161C>T	p.Asp387=	synonymous_variant	3/3	1	NM_001200.4	ENSP00000368104	P1

Frequencies

GnomAD3 genomes

AF:

0.0636

AC:

9624

AN:

151264

Hom.:

369

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0493

Gnomad AMI

AF:

0.0209

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.0317

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0255

Gnomad FIN

AF:

0.0546

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0700

Gnomad OTH

AF:

0.0675

GnomAD3 exomes

AF:

0.0695

AC:

17228

AN:

247714

Hom.:

916

AF XY:

0.0637

AC XY:

8543

AN XY:

134176

show subpopulations

Gnomad AFR exome

AF:

0.0487

Gnomad AMR exome

AF:

0.177

Gnomad ASJ exome

AF:

0.0303

Gnomad EAS exome

AF:

0.000762

Gnomad SAS exome

AF:

0.0230

Gnomad FIN exome

AF:

0.0592

Gnomad NFE exome

AF:

0.0687

Gnomad OTH exome

AF:

0.0703

GnomAD4 exome

AF:

0.0670

AC:

97699

AN:

1458938

Hom.:

3818

Cov.:

AF XY:

0.0652

AC XY:

47295

AN XY:

725832

show subpopulations

Gnomad4 AFR exome

AF:

0.0467

Gnomad4 AMR exome

AF:

0.170

Gnomad4 ASJ exome

AF:

0.0334

Gnomad4 EAS exome

AF:

0.000302

Gnomad4 SAS exome

AF:

0.0251

Gnomad4 FIN exome

AF:

0.0608

Gnomad4 NFE exome

AF:

0.0705

Gnomad4 OTH exome

AF:

0.0632

GnomAD4 genome

AF:

0.0637

AC:

9640

AN:

151370

Hom.:

373

Cov.:

AF XY:

0.0632

AC XY:

4669

AN XY:

73918

show subpopulations

Gnomad4 AFR

AF:

0.0494

Gnomad4 AMR

AF:

0.124

Gnomad4 ASJ

AF:

0.0317

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0256

Gnomad4 FIN

AF:

0.0546

Gnomad4 NFE

AF:

0.0700

Gnomad4 OTH

AF:

0.0669

Alfa

AF:

0.0596

Hom.:

146

Bravo

AF:

0.0699

Asia WGS

AF:

0.0160

AC:

AN:

3478

EpiCase

AF:

0.0651

EpiControl

AF:

0.0637

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 03, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

7.9

DANN

Benign

0.64

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over