chr15-52389376-A-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001382347.1(MYO5A):c.1543-13T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.983 in 1,602,854 control chromosomes in the GnomAD database, including 774,133 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.93 ( 64826 hom., cov: 30)
Exomes 𝑓: 0.99 ( 709307 hom. )
Consequence
MYO5A
NM_001382347.1 splice_polypyrimidine_tract, intron
NM_001382347.1 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.62
Genes affected
MYO5A (HGNC:7602): (myosin VA) This gene is one of three myosin V heavy-chain genes, belonging to the myosin gene superfamily. Myosin V is a class of actin-based motor proteins involved in cytoplasmic vesicle transport and anchorage, spindle-pole alignment and mRNA translocation. The protein encoded by this gene is abundant in melanocytes and nerve cells. Mutations in this gene cause Griscelli syndrome type-1 (GS1) and neuroectodermal melanolysosomal disease, or Elejalde disease. [provided by RefSeq, Sep 2023]
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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=-0.87).
BP6
Variant 15-52389376-A-G is Benign according to our data. Variant chr15-52389376-A-G is described in ClinVar as [Benign]. Clinvar id is 255639.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-52389376-A-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO5A | NM_001382347.1 | c.1543-13T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000399233.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO5A | ENST00000399233.7 | c.1543-13T>C | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001382347.1 |
Frequencies
GnomAD3 genomes AF: 0.933 AC: 139141AN: 149212Hom.: 64799 Cov.: 30
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GnomAD3 exomes AF: 0.969 AC: 240664AN: 248428Hom.: 117205 AF XY: 0.971 AC XY: 130788AN XY: 134704
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GnomAD4 exome AF: 0.988 AC: 1435844AN: 1453544Hom.: 709307 Cov.: 34 AF XY: 0.987 AC XY: 714208AN XY: 723470
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GnomAD4 genome AF: 0.932 AC: 139215AN: 149310Hom.: 64826 Cov.: 30 AF XY: 0.934 AC XY: 68268AN XY: 73068
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Griscelli syndrome type 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at