chr17-10629585-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002470.4(MYH3):c.5796+12A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000193 in 1,612,632 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00020 ( 3 hom. )
Consequence
MYH3
NM_002470.4 intron
NM_002470.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0640
Genes affected
MYH3 (HGNC:7573): (myosin heavy chain 3) Myosin is a major contractile protein which converts chemical energy into mechanical energy through the hydrolysis of ATP. Myosin is a hexameric protein composed of a pair of myosin heavy chains (MYH) and two pairs of nonidentical light chains. This gene is a member of the MYH family and encodes a protein with an IQ domain and a myosin head-like domain. Mutations in this gene have been associated with two congenital contracture (arthrogryposis) syndromes, Freeman-Sheldon syndrome and Sheldon-Hall syndrome. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 17-10629585-T-C is Benign according to our data. Variant chr17-10629585-T-C is described in ClinVar as [Benign]. Clinvar id is 1601146.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 26 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH3 | NM_002470.4 | c.5796+12A>G | intron_variant | ENST00000583535.6 | |||
MYH3 | XM_011523870.4 | c.5796+12A>G | intron_variant | ||||
MYH3 | XM_011523871.3 | c.5796+12A>G | intron_variant | ||||
MYH3 | XM_047436127.1 | c.5796+12A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH3 | ENST00000583535.6 | c.5796+12A>G | intron_variant | 5 | NM_002470.4 | P1 | |||
MYH3 | ENST00000577963.1 | n.338+12A>G | intron_variant, non_coding_transcript_variant | 2 | |||||
MYH3 | ENST00000579928.2 | n.326+12A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 152124Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000219 AC: 55AN: 251272Hom.: 2 AF XY: 0.000162 AC XY: 22AN XY: 135832
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GnomAD4 exome AF: 0.000197 AC: 287AN: 1460390Hom.: 3 Cov.: 37 AF XY: 0.000193 AC XY: 140AN XY: 726476
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
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Name
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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