5-38917567-T-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_003999.3(OSMR):c.1307T>A(p.Val436Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00339 in 1,613,678 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V436I) has been classified as Uncertain significance.
Frequency
Consequence
NM_003999.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OSMR | NM_003999.3 | c.1307T>A | p.Val436Asp | missense_variant | 10/18 | ENST00000274276.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OSMR | ENST00000274276.8 | c.1307T>A | p.Val436Asp | missense_variant | 10/18 | 1 | NM_003999.3 | P1 | |
OSMR | ENST00000513831.1 | c.128T>A | p.Val43Asp | missense_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00227 AC: 346AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00232 AC: 584AN: 251456Hom.: 2 AF XY: 0.00222 AC XY: 302AN XY: 135894
GnomAD4 exome AF: 0.00351 AC: 5125AN: 1461336Hom.: 14 Cov.: 31 AF XY: 0.00326 AC XY: 2372AN XY: 726986
GnomAD4 genome AF: 0.00227 AC: 346AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.00197 AC XY: 147AN XY: 74494
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | OSMR: BP4, BS1, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Apr 12, 2019 | In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge - |
OSMR-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 04, 2020 | 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