rs170986

chr20-6779784-C-A

Variant summary

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

The NM_001200.4(BMP2):c.*695C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,412 control chromosomes in the GnomAD database, including 3,621 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 0.20 (3618 hom., cov: 32)
  • Exomes 𝑓: 0.12 (3 hom.)
• Consequence: BMP2 NM_001200.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BMP2	NM_001200.4	c.*695C>A		3_prime_UTR_variant	3/3	ENST00000378827.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BMP2	ENST00000378827.5	c.*695C>A		3_prime_UTR_variant	3/3	1	NM_001200.4	P1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30508 AN: 151984 Hom.: 3616 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.00539

Gnomad SAS AF: 0.0708

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.191

GnomAD4 exome AF: 0.116 AC: 36 AN: 310 Hom.: 3 Cov.: 0 AF XY: 0.126 AC XY: 23 AN XY: 182

Gnomad4 FIN exome AF: 0.118

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.201 AC: 30532 AN: 152102 Hom.: 3618 Cov.: 32 AF XY: 0.194 AC XY: 14418 AN XY: 74366

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.00540

Gnomad4 SAS AF: 0.0713

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.190

Alfa AF: 0.175 Hom.: 2620

Bravo AF: 0.219

Asia WGS AF: 0.0690 AC: 241 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.38
Dann	Benign	0.53

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: rs170986; hg19: chr20-6760431;