NM_053025.4:c.5369-10T>G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_053025.4(MYLK):c.5369-10T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000936 in 1,614,016 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_053025.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000199 AC: 50AN: 250658Hom.: 0 AF XY: 0.000192 AC XY: 26AN XY: 135526
GnomAD4 exome AF: 0.0000944 AC: 138AN: 1461664Hom.: 0 Cov.: 31 AF XY: 0.0000880 AC XY: 64AN XY: 727132
GnomAD4 genome AF: 0.0000853 AC: 13AN: 152352Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74506
ClinVar
Submissions by phenotype
not provided Uncertain:1
Has not been previously published as pathogenic or benign to our knowledge; Reported in ClinVar as a variant of uncertain clinical significance and as a likely benign variant by other clinical laboratories (ClinVar Variant ID# 415770; Landrum et al., 2016); In-silico analysis, which includes splice predictors and evolutionary conservation, 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 -
Connective tissue disorder Uncertain:1
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Aortic aneurysm, familial thoracic 7 Benign:1
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MYLK-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at