chr15-52391996-A-G
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6BP7BS1
The NM_001382347.1(MYO5A):āc.1476T>Cā(p.Asn492Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000993 in 1,611,526 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: š 0.000085 ( 0 hom., cov: 32)
Exomes š: 0.0000021 ( 0 hom. )
Consequence
MYO5A
NM_001382347.1 synonymous
NM_001382347.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.48
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 -8 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 15-52391996-A-G is Benign according to our data. Variant chr15-52391996-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 211570.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
BP7
Synonymous conserved (PhyloP=1.48 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0000855 (13/152106) while in subpopulation AFR AF= 0.000314 (13/41424). AF 95% confidence interval is 0.000185. There are 0 homozygotes in gnomad4. There are 8 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYO5A | NM_001382347.1 | c.1476T>C | p.Asn492Asn | synonymous_variant | 12/42 | ENST00000399233.7 | NP_001369276.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO5A | ENST00000399233.7 | c.1476T>C | p.Asn492Asn | synonymous_variant | 12/42 | 5 | NM_001382347.1 | ENSP00000382179.4 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152106Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248892Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135070
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GnomAD4 exome AF: 0.00000206 AC: 3AN: 1459420Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726226
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GnomAD4 genome AF: 0.0000855 AC: 13AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74288
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 14, 2015 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 09, 2021 | - - |
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