rs35117676
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003999.3(OSMR):c.1090T>C(p.Tyr364His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 1,614,040 control chromosomes in the GnomAD database, including 150 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0085 ( 7 hom., cov: 33)
Exomes 𝑓: 0.013 ( 143 hom. )
Consequence
OSMR
NM_003999.3 missense
NM_003999.3 missense
Scores
1
1
16
Clinical Significance
Conservation
PhyloP100: -0.0290
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.01022765).
BP6
?
Variant 5-38903980-T-C is Benign according to our data. Variant chr5-38903980-T-C is described in ClinVar as [Benign]. Clinvar id is 791577.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 7 SD gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OSMR | NM_003999.3 | c.1090T>C | p.Tyr364His | missense_variant | 8/18 | ENST00000274276.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OSMR | ENST00000274276.8 | c.1090T>C | p.Tyr364His | missense_variant | 8/18 | 1 | NM_003999.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00850 AC: 1293AN: 152188Hom.: 7 Cov.: 33
GnomAD3 genomes
?
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33
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GnomAD3 exomes AF: 0.00868 AC: 2180AN: 251192Hom.: 17 AF XY: 0.00877 AC XY: 1191AN XY: 135786
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GnomAD4 exome AF: 0.0126 AC: 18358AN: 1461734Hom.: 143 Cov.: 33 AF XY: 0.0121 AC XY: 8828AN XY: 727168
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GnomAD4 genome ? AF: 0.00849 AC: 1293AN: 152306Hom.: 7 Cov.: 33 AF XY: 0.00838 AC XY: 624AN XY: 74490
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57
ESP6500AA
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ExAC
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1086
Asia WGS
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Uncertain
D
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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