5-137870288-G-GACAC
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_006790.3(MYOT):c.-211-117_-211-114dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.16 ( 1843 hom., cov: 0)
Consequence
MYOT
NM_006790.3 intron
NM_006790.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.00
Genes affected
MYOT (HGNC:12399): (myotilin) This gene encodes a cystoskeletal protein which plays a significant role in the stability of thin filaments during muscle contraction. This protein binds F-actin, crosslinks actin filaments, and prevents latrunculin A-induced filament disassembly. Mutations in this gene have been associated with limb-girdle muscular dystrophy and myofibrillar myopathies. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined.[provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 5-137870288-G-GACAC is Benign according to our data. Variant chr5-137870288-G-GACAC is described in ClinVar as [Benign]. Clinvar id is 1225913.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYOT | NM_006790.3 | c.-211-117_-211-114dup | intron_variant | ENST00000239926.9 | |||
PKD2L2-DT | XR_948815.3 | n.303-11026_303-11025insGTGT | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYOT | ENST00000239926.9 | c.-211-117_-211-114dup | intron_variant | 1 | NM_006790.3 | P1 | |||
PKD2L2-DT | ENST00000514616.6 | n.320-11026_320-11025insGTGT | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.161 AC: 20468AN: 126754Hom.: 1838 Cov.: 0
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.161 AC: 20481AN: 126828Hom.: 1843 Cov.: 0 AF XY: 0.166 AC XY: 9980AN XY: 60106
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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 | GeneDx | Aug 06, 2019 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at