Genetic Variant MYH13:p.Gln819Gln (chr17-10328100-C-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_003802.3(MYH13):c.2457G>A(p.Gln819Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 1,613,528 control chromosomes in the GnomAD database, including 33,039 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.20 ( 3464 hom., cov: 31)

Exomes 𝑓: 0.19 ( 29575 hom. )

Consequence

MYH13
NM_003802.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.728

Publications

13 publications found

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:

MYHAS (HGNC:50609): (myosin heavy chain gene cluster antisense RNA) Predicted to enable primary miRNA binding activity. Predicted to be involved in response to muscle activity and skeletal muscle fiber development. Predicted to act upstream of or within with a positive effect on gene expression. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

MYHAS links:

LOC107985004 (HGNC:):

LOC107985004 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYH13	NM_003802.3 link	c.2457G>A	p.Gln819Gln	synonymous_variant	Exon 22 of 41	ENST00000252172.9	NP_003793.2	Q9UKX3
LOC107985004	XR_007065617.1 link	n.681+7588C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYH13	ENST00000252172.9 link	c.2457G>A	p.Gln819Gln	synonymous_variant	Exon 22 of 41	1	NM_003802.3	ENSP00000252172.4		Q9UKX3

Frequencies

GnomAD3 genomes

AF:

0.202

AC:

30751

AN:

151896

Hom.:

3457

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.0910

Gnomad AMR

AF:

0.217

Gnomad ASJ

AF:

0.214

Gnomad EAS

AF:

0.509

Gnomad SAS

AF:

0.287

Gnomad FIN

AF:

0.189

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.193

GnomAD2 exomes

AF:

0.231

AC:

57808

AN:

250028

AF XY:

0.229

show subpopulations

Gnomad AFR exome

AF:

0.204

Gnomad AMR exome

AF:

0.272

Gnomad ASJ exome

AF:

0.204

Gnomad EAS exome

AF:

0.518

Gnomad FIN exome

AF:

0.188

Gnomad NFE exome

AF:

0.172

Gnomad OTH exome

AF:

0.209

GnomAD4 exome

AF:

0.190

AC:

278348

AN:

1461512

Hom.:

29575

Cov.:

AF XY:

0.193

AC XY:

140355

AN XY:

727052

show subpopulations

African (AFR)

AF:

0.205

AC:

6845

AN:

33460

American (AMR)

AF:

0.262

AC:

11710

AN:

44666

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

5431

AN:

26122

East Asian (EAS)

AF:

0.488

AC:

19358

AN:

39680

South Asian (SAS)

AF:

0.288

AC:

24840

AN:

86206

European-Finnish (FIN)

AF:

0.187

AC:

10006

AN:

53416

Middle Eastern (MID)

AF:

0.276

AC:

1592

AN:

5762

European-Non Finnish (NFE)

AF:

0.168

AC:

186310

AN:

1111812

Other (OTH)

AF:

0.203

AC:

12256

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

11940

23879

35819

47758

59698

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6834

13668

20502

27336

34170

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.203

AC:

30791

AN:

152016

Hom.:

3464

Cov.:

AF XY:

0.207

AC XY:

15386

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.206

AC:

8551

AN:

41432

American (AMR)

AF:

0.217

AC:

3314

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.214

AC:

742

AN:

3470

East Asian (EAS)

AF:

0.509

AC:

2617

AN:

5142

South Asian (SAS)

AF:

0.287

AC:

1384

AN:

4822

European-Finnish (FIN)

AF:

0.189

AC:

2004

AN:

10578

Middle Eastern (MID)

AF:

0.221

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.171

AC:

11619

AN:

67968

Other (OTH)

AF:

0.195

AC:

412

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1208

2417

3625

4834

6042

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

344

688

1032

1376

1720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.184

Hom.:

2563

Bravo

AF:

0.204

Asia WGS

AF:

0.351

AC:

1222

AN:

3478

EpiCase

AF:

0.172

EpiControl

AF:

0.174

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

(source)

DANN

Benign

0.83

PhyloP100

0.73

Mutation Taster

=98/2

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.32

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.32

Position offset: -31

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over