rs749127959
Your query was ambiguous. Multiple possible variants found:
- chr6-55759124-TACACACACACAC-T
- chr6-55759124-TACACACACACAC-TACACAC
- chr6-55759124-TACACACACACAC-TACACACAC
- chr6-55759124-TACACACACACAC-TACACACACAC
- chr6-55759124-TACACACACACAC-TACACACACACACAC
- chr6-55759124-TACACACACACAC-TACACACACACACACAC
- chr6-55759124-TACACACACACAC-TACACACACACACACACAC
- chr6-55759124-TACACACACACAC-TACACACACACACACACACAC
- chr6-55759124-TACACACACACAC-TACACACACACACACACACACAC
- chr6-55759124-TACACACACACAC-TACACACACACACACACACACACAC
- chr6-55759124-TACACACACACAC-TACACACACACACACACACACACACAC
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_021073.4(BMP5):c.1105-21_1105-10delGTGTGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000457 in 437,226 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000018 ( 0 hom., cov: 12)
Exomes 𝑓: 0.0000026 ( 0 hom. )
Consequence
BMP5
NM_021073.4 intron
NM_021073.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.73
Genes affected
BMP5 (HGNC:1072): (bone morphogenetic protein 5) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer, which plays a role in bone and cartilage development. Polymorphisms in this gene may be associated with osteoarthritis in human patients. This gene is differentially regulated in multiple human cancers. This gene encodes distinct protein isoforms that may be similarly proteolytically processed. [provided by RefSeq, Jul 2016]
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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;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| BMP5 | NM_021073.4 | c.1105-21_1105-10delGTGTGTGTGTGT | intron_variant | Intron 5 of 6 | ENST00000370830.4 | NP_066551.1 | ||
| BMP5 | NM_001329754.2 | c.1104+1321_1104+1332delGTGTGTGTGTGT | intron_variant | Intron 5 of 5 | NP_001316683.1 | |||
| BMP5 | NM_001329756.2 | c.1028-3454_1028-3443delGTGTGTGTGTGT | intron_variant | Intron 4 of 4 | NP_001316685.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.0000184 AC: 1AN: 54204Hom.: 0 Cov.: 12
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GnomAD4 exome AF: 0.00000261 AC: 1AN: 383022Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 216766
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GnomAD4 genome 0.0000184 AC: 1AN: 54204Hom.: 0 Cov.: 12 AF XY: 0.0000419 AC XY: 1AN XY: 23878
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at