20-57173646-CATAAA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001719.3(BMP7):c.1036-341_1036-337del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 384,742 control chromosomes in the GnomAD database, including 48,521 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.49 (18186 hom., cov: 0)
  • Exomes 𝑓: 0.49 (30335 hom.)
• Consequence: BMP7 NM_001719.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.22

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 -10 ACMG points.

• BP6: Variant 20-57173646-CATAAA-C is Benign according to our data. Variant chr20-57173646-CATAAA-C is described in ClinVar as [Benign]. Clinvar id is 1249651.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BMP7	NM_001719.3	c.1036-341_1036-337del		intron_variant		ENST00000395863.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BMP7	ENST00000395863.8	c.1036-341_1036-337del		intron_variant		1	NM_001719.3	P1

Frequencies

GnomAD3 genomes AF: 0.488 AC: 73873 AN: 151278 Hom.: 18162 Cov.: 0

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.511

GnomAD4 exome AF: 0.490 AC: 114384 AN: 233350 Hom.: 30335 AF XY: 0.503 AC XY: 61676 AN XY: 122652

Gnomad4 AFR exome AF: 0.479

Gnomad4 AMR exome AF: 0.569

Gnomad4 ASJ exome AF: 0.540

Gnomad4 EAS exome AF: 0.295

Gnomad4 SAS exome AF: 0.654

Gnomad4 FIN exome AF: 0.402

Gnomad4 NFE exome AF: 0.472

Gnomad4 OTH exome AF: 0.487

GnomAD4 genome AF: 0.488 AC: 73950 AN: 151392 Hom.: 18186 Cov.: 0 AF XY: 0.488 AC XY: 36081 AN XY: 73942

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.514

Alfa AF: 0.482 Hom.: 2097

Bravo AF: 0.494

Asia WGS AF: 0.510 AC: 1777 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3067075; hg19: chr20-55748702;