8-22165465-C-A
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_006129.5(BMP1):c.60C>A(p.Gly20=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000443 in 1,580,900 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 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000042 ( 0 hom. )
Consequence
BMP1
NM_006129.5 synonymous
NM_006129.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.154
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 Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.23).
BP6
?
Variant 8-22165465-C-A is Benign according to our data. Variant chr8-22165465-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2993724.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.154 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMP1 | NM_006129.5 | c.60C>A | p.Gly20= | synonymous_variant | 1/20 | ENST00000306385.10 | |
BMP1 | NM_001199.4 | c.60C>A | p.Gly20= | synonymous_variant | 1/16 | ENST00000306349.13 | |
BMP1 | NR_033403.2 | n.94C>A | non_coding_transcript_exon_variant | 1/20 | |||
BMP1 | NR_033404.2 | n.94C>A | non_coding_transcript_exon_variant | 1/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMP1 | ENST00000306385.10 | c.60C>A | p.Gly20= | synonymous_variant | 1/20 | 1 | NM_006129.5 | P1 | |
BMP1 | ENST00000306349.13 | c.60C>A | p.Gly20= | synonymous_variant | 1/16 | 1 | NM_001199.4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000147 AC: 3AN: 203772Hom.: 0 AF XY: 0.00000875 AC XY: 1AN XY: 114308
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GnomAD4 exome AF: 0.00000420 AC: 6AN: 1428722Hom.: 0 Cov.: 32 AF XY: 0.00000422 AC XY: 3AN XY: 710762
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GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74338
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 10, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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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