chr5-38881526-G-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003999.3(OSMR):c.247-67G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 1,612,720 control chromosomes in the GnomAD database, including 45,318 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 0.27 ( 6005 hom., cov: 33)
Exomes 𝑓: 0.23 ( 39313 hom. )
Consequence
OSMR
NM_003999.3 intron
NM_003999.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.411
Genes affected
OSMR (HGNC:8507): (oncostatin M receptor) This gene encodes a member of the type I cytokine receptor family. The encoded protein heterodimerizes with interleukin 6 signal transducer to form the type II oncostatin M receptor and with interleukin 31 receptor A to form the interleukin 31 receptor, and thus transduces oncostatin M and interleukin 31 induced signaling events. Mutations in this gene have been associated with familial primary localized cutaneous amyloidosis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OSMR | NM_003999.3 | c.247-67G>T | intron_variant | ENST00000274276.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OSMR | ENST00000274276.8 | c.247-67G>T | intron_variant | 1 | NM_003999.3 | P1 | |||
OSMR | ENST00000502536.5 | c.247-67G>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.268 AC: 40710AN: 152016Hom.: 6006 Cov.: 33
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GnomAD4 exome AF: 0.226 AC: 330290AN: 1460586Hom.: 39313 Cov.: 34 AF XY: 0.225 AC XY: 163781AN XY: 726596
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GnomAD4 genome ? AF: 0.268 AC: 40729AN: 152134Hom.: 6005 Cov.: 33 AF XY: 0.268 AC XY: 19904AN XY: 74372
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at