9-92419851-G-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005014.3(OMD):c.-16-2277C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.891 in 152,214 control chromosomes in the GnomAD database, including 60,559 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 0.89 ( 60559 hom., cov: 32)
Consequence
OMD
NM_005014.3 intron
NM_005014.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.763
Genes affected
OMD (HGNC:8134): (osteomodulin) Predicted to be involved in cell adhesion and regulation of bone mineralization. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
CENPP (HGNC:32933): (centromere protein P) CENPP is a subunit of a CENPH (MIM 605607)-CENPI (MIM 300065)-associated centromeric complex that targets CENPA (MIM 117139) to centromeres and is required for proper kinetochore function and mitotic progression (Okada et al., 2006 [PubMed 16622420]).[supplied by OMIM, Mar 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=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OMD | NM_005014.3 | c.-16-2277C>G | intron_variant | ENST00000375550.5 | NP_005005.1 | |||
CENPP | NM_001012267.3 | c.564+39992G>C | intron_variant | ENST00000375587.8 | NP_001012267.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OMD | ENST00000375550.5 | c.-16-2277C>G | intron_variant | 1 | NM_005014.3 | ENSP00000364700.4 | ||||
CENPP | ENST00000375587.8 | c.564+39992G>C | intron_variant | 1 | NM_001012267.3 | ENSP00000364737.3 |
Frequencies
GnomAD3 genomes AF: 0.891 AC: 135504AN: 152096Hom.: 60512 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.891 AC: 135607AN: 152214Hom.: 60559 Cov.: 32 AF XY: 0.886 AC XY: 65902AN XY: 74398
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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