17-1467459-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001080779.2(MYO1C):c.3065+21G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0506 in 1,610,758 control chromosomes in the GnomAD database, including 2,418 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.037 ( 170 hom., cov: 29)
Exomes 𝑓: 0.052 ( 2248 hom. )
Consequence
MYO1C
NM_001080779.2 intron
NM_001080779.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.20
Genes affected
MYO1C (HGNC:7597): (myosin IC) This gene encodes a member of the unconventional myosin protein family, which are actin-based molecular motors. The protein is found in the cytoplasm, and one isoform with a unique N-terminus is also found in the nucleus. The nuclear isoform associates with RNA polymerase I and II and functions in transcription initiation. The mouse ortholog of this protein also functions in intracellular vesicle transport to the plasma membrane. Multiple transcript variants encoding different isoforms have been found for this gene. The related gene myosin IE has been referred to as myosin IC in the literature, but it is a distinct locus on chromosome 19. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 17-1467459-C-T is Benign according to our data. Variant chr17-1467459-C-T is described in ClinVar as [Benign]. Clinvar id is 682784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0578 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYO1C | NM_001080779.2 | c.3065+21G>A | intron_variant | ENST00000648651.1 | NP_001074248.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO1C | ENST00000648651.1 | c.3065+21G>A | intron_variant | NM_001080779.2 | ENSP00000496954 |
Frequencies
GnomAD3 genomes AF: 0.0371 AC: 5630AN: 151864Hom.: 170 Cov.: 29
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GnomAD3 exomes AF: 0.0379 AC: 9366AN: 246894Hom.: 254 AF XY: 0.0372 AC XY: 4997AN XY: 134274
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GnomAD4 exome AF: 0.0520 AC: 75877AN: 1458776Hom.: 2248 Cov.: 35 AF XY: 0.0508 AC XY: 36906AN XY: 725866
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GnomAD4 genome AF: 0.0370 AC: 5628AN: 151982Hom.: 170 Cov.: 29 AF XY: 0.0346 AC XY: 2567AN XY: 74290
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 13, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at