chr20-57177624-A-T

Position:

• chr20-57177624-A-T

Variant summary

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

The NM_001719.3(BMP7):​c.959-2617T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,134 control chromosomes in the GnomAD database, including 15,095 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 0.42 (15095 hom., cov: 33)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: BMP7 NM_001719.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BMP7	NM_001719.3	c.959-2617T>A		intron_variant		ENST00000395863.8	NP_001710.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BMP7	ENST00000395863.8	c.959-2617T>A		intron_variant		1	NM_001719.3	ENSP00000379204	P1

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64394 AN: 152012 Hom.: 15107 Cov.: 33

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.432

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.423 AC: 64379 AN: 152130 Hom.: 15095 Cov.: 33 AF XY: 0.428 AC XY: 31827 AN XY: 74386

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.428

Alfa AF: 0.462 Hom.: 2109

Bravo AF: 0.404

Asia WGS AF: 0.447 AC: 1553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.66

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: rs6070008; hg19: chr20-55752680;