chr17-10547738-C-T
Variant summary
Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_017534.6(MYH2):c.183G>A(p.Thr61Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0101 in 1,614,188 control chromosomes in the GnomAD database, including 113 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_017534.6 synonymous
Scores
Clinical Significance
Conservation
Publications
Genome browser will be placed here
ACMG classification
Our verdict: Benign. The variant received -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH2 | NM_017534.6 | c.183G>A | p.Thr61Thr | synonymous_variant | Exon 3 of 40 | ENST00000245503.10 | NP_060004.3 | |
MYH2 | NM_001100112.2 | c.183G>A | p.Thr61Thr | synonymous_variant | Exon 3 of 40 | NP_001093582.1 | ||
MYHAS | NR_125367.1 | n.168-19799C>T | intron_variant | Intron 2 of 10 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00712 AC: 1083AN: 152188Hom.: 6 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00767 AC: 1928AN: 251408 AF XY: 0.00755 show subpopulations
GnomAD4 exome AF: 0.0104 AC: 15168AN: 1461882Hom.: 107 Cov.: 34 AF XY: 0.0101 AC XY: 7318AN XY: 727246 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00711 AC: 1083AN: 152306Hom.: 6 Cov.: 32 AF XY: 0.00683 AC XY: 509AN XY: 74490 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:4
- -
MYH2: BP4, BP7, BS1, BS2 -
- -
- -
Myopathy, proximal, and ophthalmoplegia Benign:2
- -
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not specified Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at