rs116419997
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_017534.6(MYH2):āc.1068G>Cā(p.Thr356=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000399 in 1,614,028 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T356T) has been classified as Likely benign.
Frequency
Consequence
NM_017534.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH2 | NM_017534.6 | c.1068G>C | p.Thr356= | synonymous_variant | 12/40 | ENST00000245503.10 | |
MYHAS | NR_125367.1 | n.168-27530C>G | intron_variant, non_coding_transcript_variant | ||||
MYH2 | NM_001100112.2 | c.1068G>C | p.Thr356= | synonymous_variant | 12/40 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH2 | ENST00000245503.10 | c.1068G>C | p.Thr356= | synonymous_variant | 12/40 | 1 | NM_017534.6 | P1 | |
MYH2 | ENST00000532183.6 | c.1068G>C | p.Thr356= | synonymous_variant | 11/17 | 1 | |||
MYH2 | ENST00000622564.4 | c.1068G>C | p.Thr356= | synonymous_variant | 12/18 | 1 | |||
MYH2 | ENST00000397183.6 | c.1068G>C | p.Thr356= | synonymous_variant | 12/40 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00214 AC: 326AN: 152072Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000577 AC: 145AN: 251386Hom.: 0 AF XY: 0.000449 AC XY: 61AN XY: 135858
GnomAD4 exome AF: 0.000215 AC: 315AN: 1461838Hom.: 0 Cov.: 32 AF XY: 0.000190 AC XY: 138AN XY: 727222
GnomAD4 genome ? AF: 0.00216 AC: 329AN: 152190Hom.: 1 Cov.: 32 AF XY: 0.00214 AC XY: 159AN XY: 74394
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 10, 2021 | Has not been previously published as pathogenic or benign to our knowledge; In-silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown. - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | MYH2: BP4, BP7 - |
Myopathy, proximal, and ophthalmoplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at