19-50210398-G-C

Variant summary

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

The NM_001145809.2(MYH14):c.33G>C(p.Arg11=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0275 in 1,580,478 control chromosomes in the GnomAD database, including 730 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. R11R) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.032 ( 100 hom., cov: 32)

Exomes 𝑓: 0.027 ( 630 hom. )

Consequence

MYH14
NM_001145809.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: 1.62

Variant links:

Genes affected

MYH14 (HGNC:23212): (myosin heavy chain 14) This gene encodes a member of the myosin superfamily. The protein represents a conventional non-muscle myosin; it should not be confused with the unconventional myosin-14 (MYO14). Myosins are actin-dependent motor proteins with diverse functions including regulation of cytokinesis, cell motility, and cell polarity. Mutations in this gene result in one form of autosomal dominant hearing impairment. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

MYH14 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=-0.51).

BP6

Variant 19-50210398-G-C is Benign according to our data. Variant chr19-50210398-G-C is described in ClinVar as [Benign]. Clinvar id is 44065.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-50210398-G-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=1.62 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
MYH14	NM_001145809.2 linkuse as main transcript	c.33G>C	p.Arg11=	synonymous_variant	2/43	ENST00000642316.2
MYH14	NM_001077186.2 linkuse as main transcript	c.33G>C	p.Arg11=	synonymous_variant	2/42
MYH14	NM_024729.4 linkuse as main transcript	c.33G>C	p.Arg11=	synonymous_variant	2/41

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYH14	ENST00000642316.2 linkuse as main transcript	c.33G>C	p.Arg11=	synonymous_variant	2/43		NM_001145809.2		Q7Z406-2

Frequencies

GnomAD3 genomes

AF:

0.0316

AC:

4806

AN:

152122

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0479

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.0188

Gnomad ASJ

AF:

0.0579

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0165

Gnomad FIN

AF:

0.0283

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0271

Gnomad OTH

AF:

0.0312

GnomAD3 exomes

AF:

0.0241

AC:

4594

AN:

190242

Hom.:

AF XY:

0.0245

AC XY:

2585

AN XY:

105366

show subpopulations

Gnomad AFR exome

AF:

0.0474

Gnomad AMR exome

AF:

0.0146

Gnomad ASJ exome

AF:

0.0498

Gnomad EAS exome

AF:

0.0000704

Gnomad SAS exome

AF:

0.0148

Gnomad FIN exome

AF:

0.0280

Gnomad NFE exome

AF:

0.0286

Gnomad OTH exome

AF:

0.0289

GnomAD4 exome

AF:

0.0271

AC:

38679

AN:

1428238

Hom.:

630

Cov.:

AF XY:

0.0269

AC XY:

19053

AN XY:

708706

show subpopulations

Gnomad4 AFR exome

AF:

0.0542

Gnomad4 AMR exome

AF:

0.0150

Gnomad4 ASJ exome

AF:

0.0504

Gnomad4 EAS exome

AF:

0.0000806

Gnomad4 SAS exome

AF:

0.0153

Gnomad4 FIN exome

AF:

0.0291

Gnomad4 NFE exome

AF:

0.0277

Gnomad4 OTH exome

AF:

0.0291

GnomAD4 genome

AF:

0.0316

AC:

4814

AN:

152240

Hom.:

100

Cov.:

AF XY:

0.0319

AC XY:

2377

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.0480

Gnomad4 AMR

AF:

0.0188

Gnomad4 ASJ

AF:

0.0579

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.0163

Gnomad4 FIN

AF:

0.0283

Gnomad4 NFE

AF:

0.0271

Gnomad4 OTH

AF:

0.0308

Alfa

AF:

0.0226

Hom.:

Bravo

AF:

0.0317

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:6

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 03, 2017	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Apr 30, 2012	Arg11Arg in Exon 02 of MYH14: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 3.9% (94/2438) of Afri can American chromosomes from a broad population by the NHLBI Exome Sequencing P roject (http://evs.gs.washington.edu/EVS; dbSNP rs8106196). -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Aug 05, 2014	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 11, 2023	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 29, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Feb 18, 2019	- -

Autosomal dominant nonsyndromic hearing loss 4A

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

Cadd

Benign

Dann

Benign

0.69

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