Genetic Variant MYORG:c.*95delC (chr9-34370703-TG-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_020702.5(MYORG):c.*95delC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.75 ( 43272 hom., cov: 0)

Exomes 𝑓: 0.79 ( 408838 hom. )

Consequence

MYORG
NM_020702.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.181

Publications

5 publications found

Variant links:

Genes affected

MYORG (HGNC:19918): (myogenesis regulating glycosidase (putative)) Predicted to enable hydrolase activity, hydrolyzing O-glycosyl compounds. Involved in skeletal muscle fiber development. Predicted to be located in endoplasmic reticulum membrane and nuclear membrane. Implicated in basal ganglia calcification. [provided by Alliance of Genome Resources, Apr 2022]

MYORG Gene-Disease associations (from GenCC):

basal ganglia calcification, idiopathic, 7, autosomal recessive
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, Illumina, Labcorp Genetics (formerly Invitae)
bilateral striopallidodentate calcinosis
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

MYORG links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 9-34370703-TG-T is Benign according to our data. Variant chr9-34370703-TG-T is described in ClinVar as Benign. ClinVar VariationId is 1220609.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020702.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYORG	NM_020702.5	MANE Select	c.*95delC		3_prime_UTR	Exon 2 of 2	NP_065753.2	Q6NSJ0

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MYORG	ENST00000297625.8	TSL:1 MANE Select	c.*95delC	3_prime_UTR	Exon 2 of 2	ENSP00000297625.8	Q6NSJ0
MYORG	ENST00000896633.1		c.*95delC	3_prime_UTR	Exon 2 of 2	ENSP00000566692.1
MYORG	ENST00000896634.1		c.*95delC	3_prime_UTR	Exon 2 of 2	ENSP00000566693.1

Frequencies

GnomAD3 genomes

AF:

0.749

AC:

113734

AN:

151820

Hom.:

43247

Cov.:

show subpopulations

Gnomad AFR

AF:

0.626

Gnomad AMI

AF:

0.882

Gnomad AMR

AF:

0.791

Gnomad ASJ

AF:

0.721

Gnomad EAS

AF:

0.946

Gnomad SAS

AF:

0.900

Gnomad FIN

AF:

0.768

Gnomad MID

AF:

0.772

Gnomad NFE

AF:

0.785

Gnomad OTH

AF:

0.758

GnomAD4 exome

AF:

0.792

AC:

1027425

AN:

1296840

Hom.:

408838

Cov.:

AF XY:

0.794

AC XY:

498243

AN XY:

627190

show subpopulations

African (AFR)

AF:

0.631

AC:

17893

AN:

28376

American (AMR)

AF:

0.805

AC:

16707

AN:

20744

Ashkenazi Jewish (ASJ)

AF:

0.729

AC:

13820

AN:

18962

East Asian (EAS)

AF:

0.949

AC:

32911

AN:

34694

South Asian (SAS)

AF:

0.891

AC:

56152

AN:

63026

European-Finnish (FIN)

AF:

0.768

AC:

34666

AN:

45126

Middle Eastern (MID)

AF:

0.776

AC:

3488

AN:

4496

European-Non Finnish (NFE)

AF:

0.788

AC:

809660

AN:

1027978

Other (OTH)

AF:

0.788

AC:

42128

AN:

53438

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

10481

20963

31444

41926

52407

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20160

40320

60480

80640

100800

<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:

0.749

AC:

113811

AN:

151938

Hom.:

43272

Cov.:

AF XY:

0.754

AC XY:

56026

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.626

AC:

25916

AN:

41376

American (AMR)

AF:

0.791

AC:

12087

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.721

AC:

2496

AN:

3462

East Asian (EAS)

AF:

0.945

AC:

4886

AN:

5168

South Asian (SAS)

AF:

0.900

AC:

4346

AN:

4830

European-Finnish (FIN)

AF:

0.768

AC:

8119

AN:

10566

Middle Eastern (MID)

AF:

0.765

AC:

225

AN:

294

European-Non Finnish (NFE)

AF:

0.785

AC:

53332

AN:

67950

Other (OTH)

AF:

0.759

AC:

1600

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1413

2827

4240

5654

7067

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

850

1700

2550

3400

4250

<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:

0.759

Hom.:

4725

Bravo

AF:

0.740

Asia WGS

AF:

0.900

AC:

3129

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.18

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over