Variant 17-10315796-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003802.3(MYH13):c.3881G>A(p.Arg1294Gln) variant causes a missense change. The variant allele was found at a frequency of 0.16 in 1,613,796 control chromosomes in the GnomAD database, including 21,506 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.13 ( 1566 hom., cov: 32)

Exomes 𝑓: 0.16 ( 19940 hom. )

Consequence

MYH13
NM_003802.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.19

Variant links:

Genes affected

MYH13 (HGNC:7571): (myosin heavy chain 13) Predicted to enable microfilament motor activity. Predicted to be involved in muscle contraction. Predicted to act upstream of or within cellular response to starvation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

MYH13 links:

ENSG00000273388 (HGNC:):

ENSG00000273388 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0016312599).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYH13	NM_003802.3 linkuse as main transcript	c.3881G>A	p.Arg1294Gln	missense_variant	29/41	ENST00000252172.9	NP_003793.2	Q9UKX3
LOC107985004	XR_001752791.3 linkuse as main transcript	n.96-1702C>T		intron_variant
LOC107985004	XR_007065617.1 linkuse as main transcript	n.96-1702C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MYH13	ENST00000252172.9 linkuse as main transcript	c.3881G>A	p.Arg1294Gln	missense_variant	29/41	1	NM_003802.3	ENSP00000252172.4	Q9UKX3
MYH13	ENST00000621918.1 linkuse as main transcript	c.3881G>A	p.Arg1294Gln	missense_variant	27/39	1		ENSP00000480864.1	Q9UKX3
MYH13	ENST00000418404.8 linkuse as main transcript	c.3881G>A	p.Arg1294Gln	missense_variant	28/40	5		ENSP00000404570.3	Q9UKX3
ENSG00000273388	ENST00000609088.1 linkuse as main transcript	n.95-1702C>T		intron_variant		4

Frequencies

GnomAD3 genomes

AF:

0.135

AC:

20500

AN:

152050

Hom.:

1567

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0693

Gnomad AMI

AF:

0.113

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.158

Gnomad EAS

AF:

0.162

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.203

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.133

GnomAD3 exomes

AF:

0.168

AC:

41765

AN:

249214

Hom.:

3779

AF XY:

0.171

AC XY:

23151

AN XY:

135200

show subpopulations

Gnomad AFR exome

AF:

0.0680

Gnomad AMR exome

AF:

0.177

Gnomad ASJ exome

AF:

0.161

Gnomad EAS exome

AF:

0.170

Gnomad SAS exome

AF:

0.243

Gnomad FIN exome

AF:

0.192

Gnomad NFE exome

AF:

0.154

Gnomad OTH exome

AF:

0.158

GnomAD4 exome

AF:

0.162

AC:

237135

AN:

1461628

Hom.:

19940

Cov.:

AF XY:

0.164

AC XY:

119595

AN XY:

727096

show subpopulations

Gnomad4 AFR exome

AF:

0.0684

Gnomad4 AMR exome

AF:

0.171

Gnomad4 ASJ exome

AF:

0.167

Gnomad4 EAS exome

AF:

0.175

Gnomad4 SAS exome

AF:

0.240

Gnomad4 FIN exome

AF:

0.187

Gnomad4 NFE exome

AF:

0.158

Gnomad4 OTH exome

AF:

0.150

GnomAD4 genome

AF:

0.135

AC:

20491

AN:

152168

Hom.:

1566

Cov.:

AF XY:

0.139

AC XY:

10374

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.0691

Gnomad4 AMR

AF:

0.124

Gnomad4 ASJ

AF:

0.158

Gnomad4 EAS

AF:

0.162

Gnomad4 SAS

AF:

0.237

Gnomad4 FIN

AF:

0.203

Gnomad4 NFE

AF:

0.156

Gnomad4 OTH

AF:

0.131

Alfa

AF:

0.147

Hom.:

3640

Bravo

AF:

0.125

TwinsUK

AF:

0.172

AC:

637

ALSPAC

AF:

0.156

AC:

600

ESP6500AA

AF:

0.0593

AC:

236

ESP6500EA

AF:

0.153

AC:

1276

ExAC

AF:

0.164

AC:

19861

Asia WGS

AF:

0.182

AC:

636

AN:

3478

EpiCase

AF:

0.144

EpiControl

AF:

0.148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.059

BayesDel_addAF

Benign

-0.62

BayesDel_noAF

Benign

-0.52

CADD

Benign

DANN

Benign

0.82

DEOGEN2

Benign

0.093

T;T;T

Eigen

Benign

-0.91

Eigen_PC

Benign

-0.66

FATHMM_MKL

Benign

0.095

LIST_S2

Benign

0.68

.;T;.

MetaRNN

Benign

0.0016

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-1.4

N;N;N

PrimateAI

Benign

0.32

PROVEAN

Benign

1.6

.;.;N

REVEL

Benign

0.16

Sift

Benign

1.0

.;.;T

Sift4G

Benign

1.0

T;T;T

Polyphen

0.0

B;B;B

Vest4

0.048

MPC

0.11

ClinPred

0.027

GERP RS

3.0

Varity_R

0.046

gMVP

0.11

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over