Variant chr15-52313664-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001382347.1(MYO5A):c.*32T>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 0.0216 in 1,612,714 control chromosomes in the GnomAD database, including 3,704 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.086 ( 1755 hom., cov: 33)

Exomes 𝑓: 0.015 ( 1949 hom. )

Consequence

MYO5A
NM_001382347.1 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.776

Variant links:

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]

MYO5A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 15-52313664-A-G is Benign according to our data. Variant chr15-52313664-A-G is described in ClinVar as [Benign]. Clinvar id is 1280102.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO5A	NM_001382347.1 linkuse as main transcript	c.*32T>C		3_prime_UTR_variant	42/42	ENST00000399233.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO5A	ENST00000399233.7 linkuse as main transcript	c.*32T>C		3_prime_UTR_variant	42/42	5	NM_001382347.1		Q9Y4I1-3

Frequencies

GnomAD3 genomes

AF:

0.0861

AC:

13096

AN:

152044

Hom.:

1741

Cov.:

show subpopulations

Gnomad AFR

AF:

0.289

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0259

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.0212

Gnomad SAS

AF:

0.0580

Gnomad FIN

AF:

0.000565

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.00343

Gnomad OTH

AF:

0.0569

GnomAD3 exomes

AF:

0.0317

AC:

7903

AN:

249436

Hom.:

778

AF XY:

0.0292

AC XY:

3958

AN XY:

135330

show subpopulations

Gnomad AFR exome

AF:

0.299

Gnomad AMR exome

AF:

0.0122

Gnomad ASJ exome

AF:

0.00338

Gnomad EAS exome

AF:

0.0176

Gnomad SAS exome

AF:

0.0643

Gnomad FIN exome

AF:

0.000649

Gnomad NFE exome

AF:

0.00374

Gnomad OTH exome

AF:

0.0155

GnomAD4 exome

AF:

0.0148

AC:

21630

AN:

1460552

Hom.:

1949

Cov.:

AF XY:

0.0153

AC XY:

11102

AN XY:

726688

show subpopulations

Gnomad4 AFR exome

AF:

0.308

Gnomad4 AMR exome

AF:

0.0135

Gnomad4 ASJ exome

AF:

0.00337

Gnomad4 EAS exome

AF:

0.0213

Gnomad4 SAS exome

AF:

0.0603

Gnomad4 FIN exome

AF:

0.000655

Gnomad4 NFE exome

AF:

0.00259

Gnomad4 OTH exome

AF:

0.0260

GnomAD4 genome

AF:

0.0864

AC:

13149

AN:

152162

Hom.:

1755

Cov.:

AF XY:

0.0838

AC XY:

6238

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.289

Gnomad4 AMR

AF:

0.0260

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.0208

Gnomad4 SAS

AF:

0.0579

Gnomad4 FIN

AF:

0.000565

Gnomad4 NFE

AF:

0.00343

Gnomad4 OTH

AF:

0.0601

Alfa

AF:

0.0319

Hom.:

156

Bravo

AF:

0.0972

Asia WGS

AF:

0.0680

AC:

236

AN:

3478

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 20, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

9.7

DANN

Benign

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.16

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over