rs143555593
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_017534.6(MYH2):c.1416+40G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000651 in 1,613,596 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00099 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00062 ( 8 hom. )
Consequence
MYH2
NM_017534.6 intron
NM_017534.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0100
Genes affected
MYH2 (HGNC:7572): (myosin heavy chain 2) Myosins are actin-based motor proteins that function in the generation of mechanical force in eukaryotic cells. Muscle myosins are heterohexamers composed of 2 myosin heavy chains and 2 pairs of nonidentical myosin light chains. This gene encodes a member of the class II or conventional myosin heavy chains, and functions in skeletal muscle contraction. This gene is found in a cluster of myosin heavy chain genes on chromosome 17. A mutation in this gene results in inclusion body myopathy-3. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
Variant 17-10539165-C-G is Benign according to our data. Variant chr17-10539165-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 260813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High Homozygotes in GnomAdExome4 at 8 SD gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH2 | NM_017534.6 | c.1416+40G>C | intron_variant | ENST00000245503.10 | |||
MYHAS | NR_125367.1 | n.168-28372C>G | intron_variant, non_coding_transcript_variant | ||||
MYH2 | NM_001100112.2 | c.1416+40G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH2 | ENST00000245503.10 | c.1416+40G>C | intron_variant | 1 | NM_017534.6 | P1 | |||
MYH2 | ENST00000532183.6 | c.1416+40G>C | intron_variant | 1 | |||||
MYH2 | ENST00000622564.4 | c.1416+40G>C | intron_variant | 1 | |||||
MYH2 | ENST00000397183.6 | c.1416+40G>C | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00101 AC: 153AN: 152086Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00266 AC: 667AN: 251170Hom.: 3 AF XY: 0.00220 AC XY: 299AN XY: 135732
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GnomAD4 exome AF: 0.000616 AC: 900AN: 1461392Hom.: 8 Cov.: 32 AF XY: 0.000541 AC XY: 393AN XY: 727028
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GnomAD4 genome ? AF: 0.000992 AC: 151AN: 152204Hom.: 1 Cov.: 32 AF XY: 0.00106 AC XY: 79AN XY: 74398
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 03, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at