chr9-34372349-G-T
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_020702.5(MYORG):c.595C>A(p.Arg199Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0347 in 1,598,822 control chromosomes in the GnomAD database, including 1,176 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_020702.5 missense
Scores
Clinical Significance
Conservation
Publications
- basal ganglia calcification, idiopathic, 7, autosomal recessiveInheritance: AR, AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Genomics England PanelApp, Illumina
- bilateral striopallidodentate calcinosisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYORG | NM_020702.5 | c.595C>A | p.Arg199Ser | missense_variant | Exon 2 of 2 | ENST00000297625.8 | NP_065753.2 | |
MYORG | XM_011517966.4 | c.595C>A | p.Arg199Ser | missense_variant | Exon 2 of 2 | XP_011516268.1 | ||
MYORG | XM_017014930.3 | c.595C>A | p.Arg199Ser | missense_variant | Exon 2 of 2 | XP_016870419.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0290 AC: 4417AN: 152156Hom.: 101 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0297 AC: 6414AN: 215868 AF XY: 0.0295 show subpopulations
GnomAD4 exome AF: 0.0353 AC: 51004AN: 1446548Hom.: 1075 Cov.: 71 AF XY: 0.0347 AC XY: 24961AN XY: 718556 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0290 AC: 4416AN: 152274Hom.: 101 Cov.: 33 AF XY: 0.0298 AC XY: 2220AN XY: 74464 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:3
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MYORG-related disorder Benign:1
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