rs779483683
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4
The NM_053025.4(MYLK):βc.3120_3155delβ(p.Ala1044_Pro1055del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000041 in 1,461,754 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (β ). Synonymous variant affecting the same amino acid position (i.e. N1040N) has been classified as Likely benign.
Frequency
Consequence
NM_053025.4 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYLK | NM_053025.4 | c.3120_3155del | p.Ala1044_Pro1055del | inframe_deletion | 18/34 | ENST00000360304.8 | |
LOC105369194 | XR_924417.4 | n.108-3545_108-3510del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYLK | ENST00000360304.8 | c.3120_3155del | p.Ala1044_Pro1055del | inframe_deletion | 18/34 | 5 | NM_053025.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 151696Hom.: 0 Cov.: 30 FAILED QC
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251460Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135892
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461754Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 727162
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 151696Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74054
ClinVar
Submissions by phenotype
Aortic aneurysm, familial thoracic 7 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 23, 2022 | This variant, c.3120_3155del, results in the deletion of 12 amino acid(s) of the MYLK protein (p.Ala1044_Pro1055del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs779483683, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with MYLK-related conditions. ClinVar contains an entry for this variant (Variation ID: 539081). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at