3-108383733-T-TAAAA
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_014981.3(MYH15):c.5632-8_5632-5dupTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000193 in 1,034,474 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000017 ( 0 hom., cov: 29)
Exomes 𝑓: 0.000019 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MYH15
NM_014981.3 splice_region, intron
NM_014981.3 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.240
Genes affected
MYH15 (HGNC:31073): (myosin heavy chain 15) Predicted to enable several functions, including ATP binding activity; actin filament binding activity; and calmodulin binding activity. Predicted to be involved in extraocular skeletal muscle development. Located in cytosol and intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAdExome4 at 20 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH15 | NM_014981.3 | c.5632-8_5632-5dupTTTT | splice_region_variant, intron_variant | Intron 39 of 40 | ENST00000693548.1 | NP_055796.2 | ||
MYH15 | XM_011512559.3 | c.5692-8_5692-5dupTTTT | splice_region_variant, intron_variant | Intron 41 of 42 | XP_011510861.1 | |||
LOC124900545 | XR_007095998.1 | n.112+2084_112+2087dupAAAA | intron_variant | Intron 1 of 1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYH15 | ENST00000693548.1 | c.5632-5_5632-4insTTTT | splice_region_variant, intron_variant | Intron 39 of 40 | NM_014981.3 | ENSP00000508967.1 | ||||
MYH15 | ENST00000273353.5 | c.5632-5_5632-4insTTTT | splice_region_variant, intron_variant | Intron 40 of 41 | 1 | ENSP00000273353.4 | ||||
MYH15 | ENST00000689784.1 | c.4651-5_4651-4insTTTT | splice_region_variant, intron_variant | Intron 31 of 32 | ENSP00000509841.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 59468Hom.: 0 Cov.: 29 FAILED QC
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000534 AC: 3AN: 56170Hom.: 0 AF XY: 0.0000979 AC XY: 3AN XY: 30628
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GnomAD4 exome AF: 0.0000193 AC: 20AN: 1034474Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 7AN XY: 506768
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000168 AC: 1AN: 59468Hom.: 0 Cov.: 29 AF XY: 0.0000357 AC XY: 1AN XY: 28048
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Not reported inComputational scores
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at