chr17-10521326-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PP2PP3BP4_StrongBP6_Very_StrongBS2
The NM_017534.6(MYH2):c.5780G>A(p.Arg1927Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00626 in 1,614,124 control chromosomes in the GnomAD database, including 52 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. R1927R) has been classified as Likely benign.
Frequency
Consequence
NM_017534.6 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 |
---|---|---|---|---|---|---|---|
MYH2 | NM_017534.6 | c.5780G>A | p.Arg1927Gln | missense_variant | 40/40 | ENST00000245503.10 | |
MYHAS | NR_125367.1 | n.168-46211C>T | intron_variant, non_coding_transcript_variant | ||||
MYH2 | NM_001100112.2 | c.5780G>A | p.Arg1927Gln | missense_variant | 40/40 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH2 | ENST00000245503.10 | c.5780G>A | p.Arg1927Gln | missense_variant | 40/40 | 1 | NM_017534.6 | P1 | |
ENST00000399342.6 | n.207-11998C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00446 AC: 679AN: 152164Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00410 AC: 1031AN: 251444Hom.: 7 AF XY: 0.00445 AC XY: 605AN XY: 135886
GnomAD4 exome AF: 0.00644 AC: 9421AN: 1461842Hom.: 46 Cov.: 31 AF XY: 0.00629 AC XY: 4574AN XY: 727226
GnomAD4 genome AF: 0.00446 AC: 679AN: 152282Hom.: 6 Cov.: 32 AF XY: 0.00403 AC XY: 300AN XY: 74464
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2024 | MYH2: BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 23, 2020 | This variant is associated with the following publications: (PMID: 15741996) - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Nov 07, 2016 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 15, 2014 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 07, 2020 | - - |
MYH2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 09, 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). - |
Myopathy, proximal, and ophthalmoplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at