Variant chr20-57175148-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001719.3(BMP7):c.959-141C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0747 in 905,860 control chromosomes in the GnomAD database, including 2,788 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.070 ( 433 hom., cov: 33)

Exomes 𝑓: 0.076 ( 2355 hom. )

Consequence

BMP7
NM_001719.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.01

Variant links:

Genes affected

BMP7 (HGNC:1074): (bone morphogenetic protein 7) 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, kidney and brown adipose tissue development. Additionally, this protein induces ectopic bone formation and may promote fracture healing in human patients. [provided by RefSeq, Jul 2016]

BMP7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 20-57175148-G-T is Benign according to our data. Variant chr20-57175148-G-T is described in ClinVar as [Benign]. Clinvar id is 1238833.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BMP7	NM_001719.3 linkuse as main transcript	c.959-141C>A		intron_variant		ENST00000395863.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BMP7	ENST00000395863.8 linkuse as main transcript	c.959-141C>A		intron_variant		1	NM_001719.3	P1

Frequencies

GnomAD3 genomes

AF:

0.0704

AC:

10707

AN:

152140

Hom.:

433

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0549

Gnomad AMI

AF:

0.0504

Gnomad AMR

AF:

0.0502

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.0375

Gnomad SAS

AF:

0.0682

Gnomad FIN

AF:

0.100

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.0805

Gnomad OTH

AF:

0.0669

GnomAD4 exome

AF:

0.0755

AC:

56929

AN:

753602

Hom.:

2355

AF XY:

0.0750

AC XY:

29524

AN XY:

393534

show subpopulations

Gnomad4 AFR exome

AF:

0.0549

Gnomad4 AMR exome

AF:

0.0443

Gnomad4 ASJ exome

AF:

0.105

Gnomad4 EAS exome

AF:

0.0203

Gnomad4 SAS exome

AF:

0.0619

Gnomad4 FIN exome

AF:

0.100

Gnomad4 NFE exome

AF:

0.0806

Gnomad4 OTH exome

AF:

0.0808

GnomAD4 genome

AF:

0.0703

AC:

10710

AN:

152258

Hom.:

433

Cov.:

AF XY:

0.0705

AC XY:

5250

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.0550

Gnomad4 AMR

AF:

0.0501

Gnomad4 ASJ

AF:

0.112

Gnomad4 EAS

AF:

0.0378

Gnomad4 SAS

AF:

0.0676

Gnomad4 FIN

AF:

0.100

Gnomad4 NFE

AF:

0.0805

Gnomad4 OTH

AF:

0.0666

Alfa

AF:

0.0728

Hom.:

Bravo

AF:

0.0657

Asia WGS

AF:

0.0900

AC:

313

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 28, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.4

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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