rs3924231
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006129.5(BMP1):c.1180+116A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 855,576 control chromosomes in the GnomAD database, including 20,818 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.27 ( 7012 hom., cov: 33)
Exomes 𝑓: 0.18 ( 13806 hom. )
Consequence
BMP1
NM_006129.5 intron
NM_006129.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.23
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 8-22192267-A-G is Benign according to our data. Variant chr8-22192267-A-G is described in ClinVar as [Benign]. Clinvar id is 675112.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMP1 | NM_001199.4 | c.1180+116A>G | intron_variant | ENST00000306349.13 | |||
BMP1 | NM_006129.5 | c.1180+116A>G | intron_variant | ENST00000306385.10 | |||
BMP1 | NR_033403.2 | n.1251+116A>G | intron_variant, non_coding_transcript_variant | ||||
BMP1 | NR_033404.2 | n.1251+116A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMP1 | ENST00000306349.13 | c.1180+116A>G | intron_variant | 1 | NM_001199.4 | ||||
BMP1 | ENST00000306385.10 | c.1180+116A>G | intron_variant | 1 | NM_006129.5 | P1 | |||
ENST00000647689.1 | n.260+52T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.272 AC: 41350AN: 151856Hom.: 6991 Cov.: 33
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GnomAD4 exome AF: 0.184 AC: 129567AN: 703602Hom.: 13806 Cov.: 9 AF XY: 0.182 AC XY: 66029AN XY: 363790
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GnomAD4 genome ? AF: 0.273 AC: 41423AN: 151974Hom.: 7012 Cov.: 33 AF XY: 0.276 AC XY: 20534AN XY: 74290
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at