Variant rs13329278 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001382347.1(MYO5A):c.3414A>G(p.Ser1138=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0242 in 1,605,090 control chromosomes in the GnomAD database, including 4,674 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.097 ( 2246 hom., cov: 32)

Exomes 𝑓: 0.017 ( 2428 hom. )

Consequence

MYO5A
NM_001382347.1 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -1.24

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 15-52359977-T-C is Benign according to our data. Variant chr15-52359977-T-C is described in ClinVar as [Benign]. Clinvar id is 255647.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.24 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO5A	NM_001382347.1 linkuse as main transcript	c.3414A>G	p.Ser1138=	synonymous_variant	25/42	ENST00000399233.7	NP_001369276.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO5A	ENST00000399233.7 linkuse as main transcript	c.3414A>G	p.Ser1138=	synonymous_variant	25/42	5	NM_001382347.1	ENSP00000382179		Q9Y4I1-3

Frequencies

GnomAD3 genomes

AF:

0.0969

AC:

14746

AN:

152138

Hom.:

2223

Cov.:

show subpopulations

Gnomad AFR

AF:

0.325

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0292

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.0289

Gnomad SAS

AF:

0.0622

Gnomad FIN

AF:

0.000565

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.00340

Gnomad OTH

AF:

0.0617

GnomAD3 exomes

AF:

0.0351

AC:

8712

AN:

247932

Hom.:

971

AF XY:

0.0322

AC XY:

4327

AN XY:

134516

show subpopulations

Gnomad AFR exome

AF:

0.337

Gnomad AMR exome

AF:

0.0136

Gnomad ASJ exome

AF:

0.00340

Gnomad EAS exome

AF:

0.0255

Gnomad SAS exome

AF:

0.0675

Gnomad FIN exome

AF:

0.000652

Gnomad NFE exome

AF:

0.00379

Gnomad OTH exome

AF:

0.0178

GnomAD4 exome

AF:

0.0165

AC:

23997

AN:

1452834

Hom.:

2428

Cov.:

AF XY:

0.0168

AC XY:

12170

AN XY:

723206

show subpopulations

Gnomad4 AFR exome

AF:

0.347

Gnomad4 AMR exome

AF:

0.0153

Gnomad4 ASJ exome

AF:

0.00342

Gnomad4 EAS exome

AF:

0.0338

Gnomad4 SAS exome

AF:

0.0642

Gnomad4 FIN exome

AF:

0.000657

Gnomad4 NFE exome

AF:

0.00260

Gnomad4 OTH exome

AF:

0.0306

GnomAD4 genome

AF:

0.0973

AC:

14817

AN:

152256

Hom.:

2246

Cov.:

AF XY:

0.0949

AC XY:

7062

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.326

Gnomad4 AMR

AF:

0.0291

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.0282

Gnomad4 SAS

AF:

0.0616

Gnomad4 FIN

AF:

0.000565

Gnomad4 NFE

AF:

0.00340

Gnomad4 OTH

AF:

0.0682

Alfa

AF:

0.0221

Hom.:

840

Bravo

AF:

0.110

Asia WGS

AF:

0.0850

AC:

295

AN:

3478

EpiCase

AF:

0.00398

EpiControl

AF:

0.00351

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 26, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 09, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.6

DANN

Benign

0.42

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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