rs111596355

Variant names:

• chr8-22165236-A-C
• rs111596355
• ENST00000520970.5:n.-170A>C

Your query was ambiguous. Multiple possible variants found:

• chr8-22165236-A-C
• chr8-22165236-A-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000397814(BMP1):​c.-170A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: BMP1 ENST00000397814 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BMP1	NM_006129.5	c.-170A>C		upstream_gene_variant		ENST00000306385.10	NP_006120.1
BMP1	NM_001199.4	c.-170A>C		upstream_gene_variant		ENST00000306349.13	NP_001190.1
BMP1	NR_033403.2	n.-136A>C		upstream_gene_variant
BMP1	NR_033404.2	n.-136A>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BMP1	ENST00000306385.10	c.-170A>C		upstream_gene_variant		1	NM_006129.5	ENSP00000305714.5
BMP1	ENST00000306349.13	c.-170A>C		upstream_gene_variant		1	NM_001199.4	ENSP00000306121.8

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 8

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.6
DANN	Benign	0.68

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: rs111596355; hg19: chr8-22022749;