rs570950857
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBS2_Supporting
The NM_002470.4(MYH3):c.5796+29C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000062 in 1,611,958 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000063 ( 1 hom. )
Consequence
MYH3
NM_002470.4 intron
NM_002470.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.88
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 Likely_benign. Variant got -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BS2
High AC in GnomAd4 at 8 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH3 | NM_002470.4 | c.5796+29C>T | intron_variant | ENST00000583535.6 | NP_002461.2 | |||
MYH3 | XM_011523870.4 | c.5796+29C>T | intron_variant | XP_011522172.1 | ||||
MYH3 | XM_011523871.3 | c.5796+29C>T | intron_variant | XP_011522173.1 | ||||
MYH3 | XM_047436127.1 | c.5796+29C>T | intron_variant | XP_047292083.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYH3 | ENST00000583535.6 | c.5796+29C>T | intron_variant | 5 | NM_002470.4 | ENSP00000464317 | P1 | |||
MYH3 | ENST00000577963.1 | n.338+29C>T | intron_variant, non_coding_transcript_variant | 2 | ||||||
MYH3 | ENST00000579928.2 | n.326+29C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152138Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000917 AC: 23AN: 250874Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135690
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GnomAD4 exome AF: 0.0000630 AC: 92AN: 1459702Hom.: 1 Cov.: 37 AF XY: 0.0000923 AC XY: 67AN XY: 726134
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GnomAD4 genome AF: 0.0000525 AC: 8AN: 152256Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74452
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at