8-22165438-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_006129.5(BMP1):c.33C>T(p.Leu11=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000965 in 1,564,570 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 Likely benign (★★).
Frequency
Genomes: 𝑓 0.00054 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000048 ( 0 hom. )
Consequence
BMP1
NM_006129.5 synonymous
NM_006129.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.152
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 -15 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant 8-22165438-C-T is Benign according to our data. Variant chr8-22165438-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 512914.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.152 with no splicing effect.
BS1
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Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000545 (83/152304) while in subpopulation AFR AF= 0.00192 (80/41584). AF 95% confidence interval is 0.00158. There are 0 homozygotes in gnomad4. There are 42 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMP1 | NM_006129.5 | c.33C>T | p.Leu11= | synonymous_variant | 1/20 | ENST00000306385.10 | |
BMP1 | NM_001199.4 | c.33C>T | p.Leu11= | synonymous_variant | 1/16 | ENST00000306349.13 | |
BMP1 | NR_033403.2 | n.67C>T | non_coding_transcript_exon_variant | 1/20 | |||
BMP1 | NR_033404.2 | n.67C>T | non_coding_transcript_exon_variant | 1/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMP1 | ENST00000306385.10 | c.33C>T | p.Leu11= | synonymous_variant | 1/20 | 1 | NM_006129.5 | P1 | |
BMP1 | ENST00000306349.13 | c.33C>T | p.Leu11= | synonymous_variant | 1/16 | 1 | NM_001199.4 |
Frequencies
GnomAD3 genomes ? AF: 0.000545 AC: 83AN: 152196Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000974 AC: 18AN: 184748Hom.: 0 AF XY: 0.0000764 AC XY: 8AN XY: 104650
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GnomAD4 exome AF: 0.0000481 AC: 68AN: 1412266Hom.: 0 Cov.: 32 AF XY: 0.0000413 AC XY: 29AN XY: 702288
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GnomAD4 genome ? AF: 0.000545 AC: 83AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.000564 AC XY: 42AN XY: 74468
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2020 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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