rs150782002
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_001382347.1(MYO5A):c.3567+20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000247 in 1,612,866 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 Benign (★★).
Frequency
Genomes: 𝑓 0.0013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00014 ( 0 hom. )
Consequence
MYO5A
NM_001382347.1 intron
NM_001382347.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.552
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 -14 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 15-52353851-G-A is Benign according to our data. Variant chr15-52353851-G-A is described in ClinVar as [Benign]. Clinvar id is 255649.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00128 (195/152342) while in subpopulation AFR AF= 0.00402 (167/41576). AF 95% confidence interval is 0.00352. There are 0 homozygotes in gnomad4. There are 78 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYO5A | NM_001382347.1 | c.3567+20C>T | intron_variant | ENST00000399233.7 | NP_001369276.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO5A | ENST00000399233.7 | c.3567+20C>T | intron_variant | 5 | NM_001382347.1 | ENSP00000382179 |
Frequencies
GnomAD3 genomes AF: 0.00128 AC: 195AN: 152224Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000270 AC: 67AN: 248432Hom.: 0 AF XY: 0.000222 AC XY: 30AN XY: 134888
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GnomAD4 exome AF: 0.000140 AC: 204AN: 1460524Hom.: 0 Cov.: 32 AF XY: 0.000116 AC XY: 84AN XY: 726634
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GnomAD4 genome AF: 0.00128 AC: 195AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.00105 AC XY: 78AN XY: 74492
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 03, 2022 | - - |
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