8-22201444-T-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4
The NM_001199.4(BMP1):c.*241T>C variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.00000852 in 1,408,594 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000088 ( 0 hom. )
Consequence
BMP1
NM_001199.4 3_prime_UTR
NM_001199.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.63
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]
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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;
PP5
Variant 8-22201444-T-C is Pathogenic according to our data. Variant chr8-22201444-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 190231.Status of the report is no_assertion_criteria_provided, 0 stars.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.25). . Strength limited to SUPPORTING due to the PP5.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMP1 | NM_001199.4 | c.*241T>C | 3_prime_UTR_variant | 16/16 | ENST00000306349.13 | ||
BMP1 | NM_006129.5 | c.2108-359T>C | intron_variant | ENST00000306385.10 | |||
BMP1 | NR_033404.2 | n.2505T>C | non_coding_transcript_exon_variant | 16/16 | |||
BMP1 | NR_033403.2 | n.2179-359T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMP1 | ENST00000306349.13 | c.*241T>C | 3_prime_UTR_variant | 16/16 | 1 | NM_001199.4 | |||
BMP1 | ENST00000306385.10 | c.2108-359T>C | intron_variant | 1 | NM_006129.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.00000876 AC: 11AN: 1256420Hom.: 0 Cov.: 33 AF XY: 0.00000658 AC XY: 4AN XY: 607904
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74346
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Osteogenesis imperfecta type 13 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 15, 2015 | - - |
Computational scores
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BayesDel_noAF
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Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at