20-57212566-G-A

Position:

• chr20-57212566-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001719.3(BMP7):​c.612-9943C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 152,094 control chromosomes in the GnomAD database, including 19,418 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 0.49 (19418 hom., cov: 33)
• Consequence: BMP7 NM_001719.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.96

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BMP7	NM_001719.3	c.612-9943C>T		intron_variant		ENST00000395863.8	NP_001710.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BMP7	ENST00000395863.8	c.612-9943C>T		intron_variant		1	NM_001719.3	ENSP00000379204	P1

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74812 AN: 151976 Hom.: 19413 Cov.: 33

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.492 AC: 74846 AN: 152094 Hom.: 19418 Cov.: 33 AF XY: 0.494 AC XY: 36730 AN XY: 74340

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.533

Alfa AF: 0.489 Hom.: 5318

Bravo AF: 0.481

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.025
DANN	Benign	0.61

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: rs12481628; hg19: chr20-55787622;