dbSNP rs750344454: BMP1:c.-251_-244delGGAGGGAG (chr8-22165142-CGGAGGGAG-C) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000397814(BMP1):c.-251_-244delGGAGGGAG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000752 in 345,962 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000033 ( 0 hom., cov: 25)

Exomes 𝑓: 0.000098 ( 0 hom. )

Consequence

BMP1
ENST00000397814 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.56

Variant links:

Genes affected

BMP1 (HGNC:1067): (bone morphogenetic protein 1) This gene encodes a protein that is capable of inducing formation of cartilage in vivo. Although other bone morphogenetic proteins are members of the TGF-beta superfamily, this gene encodes a protein that is not closely related to other known growth factors. This gene is expressed as alternatively spliced variants that share an N-terminal protease domain but differ in their C-terminal region. [provided by RefSeq, Aug 2008]

BMP1 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
BMP1	NM_006129.5 link	c.-263_-256delGGAGGGAG	upstream_gene_variant	ENST00000306385.10	NP_006120.1	P13497-1
BMP1	NM_001199.4 link	c.-263_-256delGGAGGGAG	upstream_gene_variant	ENST00000306349.13	NP_001190.1	P13497-2
BMP1	NR_033403.2 link	n.-229_-222delGGAGGGAG	upstream_gene_variant
BMP1	NR_033404.2 link	n.-229_-222delGGAGGGAG	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BMP1	ENST00000306385.10 link	c.-263_-256delGGAGGGAG		upstream_gene_variant		1	NM_006129.5	ENSP00000305714.5		P13497-1
BMP1	ENST00000306349.13 link	c.-263_-256delGGAGGGAG		upstream_gene_variant		1	NM_001199.4	ENSP00000306121.8		P13497-2

Frequencies

GnomAD3 genomes

AF:

0.0000329

AC:

AN:

121568

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000600

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000357

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000980

AC:

AN:

224394

Hom.:

AF XY:

0.0000952

AC XY:

AN XY:

115570

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000199

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000734

Gnomad4 FIN exome

AF:

0.000166

Gnomad4 NFE exome

AF:

0.000105

Gnomad4 OTH exome

AF:

0.000139

GnomAD4 genome

AF:

0.0000329

AC:

AN:

121568

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

58670

show subpopulations

Gnomad4 AFR

AF:

0.0000600

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000357

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over