rs34675408
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003999.3(OSMR):c.561T>G(p.His187Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0775 in 1,613,524 control chromosomes in the GnomAD database, including 5,554 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003999.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OSMR | NM_003999.3 | c.561T>G | p.His187Gln | missense_variant | 5/18 | ENST00000274276.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OSMR | ENST00000274276.8 | c.561T>G | p.His187Gln | missense_variant | 5/18 | 1 | NM_003999.3 | P1 | |
OSMR | ENST00000502536.5 | c.561T>G | p.His187Gln | missense_variant | 5/7 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0958 AC: 14575AN: 152142Hom.: 786 Cov.: 33
GnomAD3 exomes AF: 0.0830 AC: 20842AN: 251258Hom.: 1047 AF XY: 0.0851 AC XY: 11563AN XY: 135796
GnomAD4 exome AF: 0.0756 AC: 110424AN: 1461264Hom.: 4759 Cov.: 32 AF XY: 0.0772 AC XY: 56155AN XY: 726964
GnomAD4 genome ? AF: 0.0959 AC: 14607AN: 152260Hom.: 795 Cov.: 33 AF XY: 0.0971 AC XY: 7233AN XY: 74454
ClinVar
Submissions by phenotype
OSMR-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 15, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at