rs529829552
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2PM5PP3_StrongPP5
The NM_004560.4(ROR2):c.1970G>A(p.Arg657His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,614,174 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R657C) has been classified as Likely pathogenic.
Frequency
Consequence
NM_004560.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ROR2 | NM_004560.4 | c.1970G>A | p.Arg657His | missense_variant | 9/9 | ENST00000375708.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ROR2 | ENST00000375708.4 | c.1970G>A | p.Arg657His | missense_variant | 9/9 | 1 | NM_004560.4 | P1 | |
ROR2 | ENST00000375715.5 | c.1550G>A | p.Arg517His | missense_variant | 9/13 | 1 | |||
ROR2 | ENST00000550066.5 | n.2438G>A | non_coding_transcript_exon_variant | 11/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251352Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135870
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461852Hom.: 0 Cov.: 43 AF XY: 0.00000550 AC XY: 4AN XY: 727226
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74478
ClinVar
Submissions by phenotype
Autosomal recessive Robinow syndrome Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine | - | - - |
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | research | Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre | - | - - |
Brachydactyly, type B1Robinow syndrome, autosomal recessive Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 28, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at