chr15-52313693-C-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001382347.1(MYO5A):c.*3G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000571 in 1,614,122 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00041 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00059 ( 6 hom. )
Consequence
MYO5A
NM_001382347.1 3_prime_UTR
NM_001382347.1 3_prime_UTR
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 was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 15-52313693-C-G is Benign according to our data. Variant chr15-52313693-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 435920.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.000407 (62/152262) while in subpopulation EAS AF = 0.00636 (33/5188). AF 95% confidence interval is 0.00465. There are 2 homozygotes in GnomAd4. There are 34 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position FAILED quality control check.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYO5A | NM_001382347.1 | c.*3G>C | 3_prime_UTR_variant | Exon 42 of 42 | ENST00000399233.7 | NP_001369276.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000355 AC: 54AN: 152144Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
54
AN:
152144
Hom.:
Cov.:
33
Gnomad AFR
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GnomAD2 exomes AF: 0.000890 AC: 222AN: 249432 AF XY: 0.00103 show subpopulations
GnomAD2 exomes
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AC:
222
AN:
249432
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GnomAD4 exome AF: 0.000588 AC: 860AN: 1461860Hom.: 6 Cov.: 31 AF XY: 0.000666 AC XY: 484AN XY: 727226 show subpopulations
GnomAD4 exome
AF:
AC:
860
AN:
1461860
Hom.:
Cov.:
31
AF XY:
AC XY:
484
AN XY:
727226
Gnomad4 AFR exome
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0
AN:
33480
Gnomad4 AMR exome
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AC:
0
AN:
44724
Gnomad4 ASJ exome
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0
AN:
26136
Gnomad4 EAS exome
AF:
AC:
473
AN:
39696
Gnomad4 SAS exome
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AC:
312
AN:
86258
Gnomad4 FIN exome
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0
AN:
53416
Gnomad4 NFE exome
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AC:
2
AN:
1112000
Gnomad4 Remaining exome
AF:
AC:
72
AN:
60394
Heterozygous variant carriers
0
46
93
139
186
232
0.00
0.20
0.40
0.60
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0.95
Allele balance
Exome Het
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Age
GnomAD4 genome AF: 0.000407 AC: 62AN: 152262Hom.: 2 Cov.: 33 AF XY: 0.000457 AC XY: 34AN XY: 74446 show subpopulations
GnomAD4 genome
AF:
AC:
62
AN:
152262
Hom.:
Cov.:
33
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34
AN XY:
74446
Gnomad4 AFR
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0
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0
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0
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0
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0
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0
Gnomad4 EAS
AF:
AC:
0.00636083
AN:
0.00636083
Gnomad4 SAS
AF:
AC:
0.00394518
AN:
0.00394518
Gnomad4 FIN
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0
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0
Gnomad4 NFE
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0
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0
Gnomad4 OTH
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AC:
0.0047259
AN:
0.0047259
Heterozygous variant carriers
0
3
6
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11
14
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0.95
Allele balance
Genome Het
Variant carriers
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Alfa
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Asia WGS
AF:
AC:
34
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Jun 27, 2016
Genetic Services Laboratory, University of Chicago
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism
Splicing
Name
Calibrated prediction
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at