rs7838961
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006129.5(BMP1):c.1077+956G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 152,018 control chromosomes in the GnomAD database, including 24,050 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 0.56 ( 24050 hom., cov: 32)
Consequence
BMP1
NM_006129.5 intron
NM_006129.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.04
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMP1 | NM_001199.4 | c.1077+956G>A | intron_variant | ENST00000306349.13 | |||
BMP1 | NM_006129.5 | c.1077+956G>A | intron_variant | ENST00000306385.10 | |||
BMP1 | NR_033403.2 | n.1148+956G>A | intron_variant, non_coding_transcript_variant | ||||
BMP1 | NR_033404.2 | n.1148+956G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMP1 | ENST00000306349.13 | c.1077+956G>A | intron_variant | 1 | NM_001199.4 | ||||
BMP1 | ENST00000306385.10 | c.1077+956G>A | intron_variant | 1 | NM_006129.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.557 AC: 84572AN: 151900Hom.: 24004 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.557 AC: 84666AN: 152018Hom.: 24050 Cov.: 32 AF XY: 0.562 AC XY: 41776AN XY: 74286
GnomAD4 genome
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32
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74286
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2196
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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