Genetic Variant MYL1:c.304+75_304+80delGTGTGT (chr2-210298339-TACACAC-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_079420.3(MYL1):c.304+75_304+80delGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0013 in 1,184,146 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00081 ( 1 hom., cov: 0)

Exomes 𝑓: 0.0014 ( 1 hom. )

Consequence

MYL1
NM_079420.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.214

Publications

0 publications found

Variant links:

Genes affected

MYL1 (HGNC:7582): (myosin light chain 1) Myosin is a hexameric ATPase cellular motor protein. It is composed of two heavy chains, two nonphosphorylatable alkali light chains, and two phosphorylatable regulatory light chains. This gene encodes a myosin alkali light chain expressed in fast skeletal muscle. Two transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]

MYL1 Gene-Disease associations (from GenCC):

congenital myopathy with reduced type 2 muscle fibers
Inheritance: AR, Unknown Classification: SUPPORTIVE, LIMITED Submitted by: G2P, Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae)
congenital myopathy
Inheritance: AR Classification: LIMITED Submitted by: ClinGen

MYL1 links:

ENSG00000279317 (HGNC:):

ENSG00000279317 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_079420.3. 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
	MYL1	NM_079420.3	MANE Select	c.304+75_304+80delGTGTGT		intron	N/A	NP_524144.1	P05976-1
	MYL1	NM_079422.3		c.172+75_172+80delGTGTGT		intron	N/A	NP_524146.1	P05976-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MYL1	ENST00000352451.4	TSL:1 MANE Select	c.304+75_304+80delGTGTGT	intron	N/A	ENSP00000307280.4	P05976-1
MYL1	ENST00000341685.8	TSL:1	c.172+75_172+80delGTGTGT	intron	N/A	ENSP00000343321.4	P05976-2
MYL1	ENST00000957378.1		c.268+75_268+80delGTGTGT	intron	N/A	ENSP00000627437.1

Frequencies

GnomAD3 genomes

AF:

0.000808

AC:

119

AN:

147306

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000126

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00258

Gnomad ASJ

AF:

0.00962

Gnomad EAS

AF:

0.00245

Gnomad SAS

AF:

0.00111

Gnomad FIN

AF:

0.000102

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000374

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00137

AC:

1424

AN:

1036732

Hom.:

AF XY:

0.00134

AC XY:

706

AN XY:

528460

show subpopulations

African (AFR)

AF:

0.000800

AC:

AN:

26250

American (AMR)

AF:

0.000759

AC:

AN:

42144

Ashkenazi Jewish (ASJ)

AF:

0.00841

AC:

178

AN:

21158

East Asian (EAS)

AF:

0.00591

AC:

211

AN:

35678

South Asian (SAS)

AF:

0.00126

AC:

AN:

71452

European-Finnish (FIN)

AF:

0.000404

AC:

AN:

44528

Middle Eastern (MID)

AF:

0.00152

AC:

AN:

3952

European-Non Finnish (NFE)

AF:

0.00106

AC:

793

AN:

745860

Other (OTH)

AF:

0.00164

AC:

AN:

45710

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.401

Heterozygous variant carriers

147

221

294

368

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

102

136

170

<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:

0.000807

AC:

119

AN:

147414

Hom.:

Cov.:

AF XY:

0.000768

AC XY:

AN XY:

71624

show subpopulations

African (AFR)

AF:

0.000125

AC:

AN:

39858

American (AMR)

AF:

0.00258

AC:

AN:

14728

Ashkenazi Jewish (ASJ)

AF:

0.00962

AC:

AN:

3430

East Asian (EAS)

AF:

0.00246

AC:

AN:

4882

South Asian (SAS)

AF:

0.00111

AC:

AN:

4518

European-Finnish (FIN)

AF:

0.000102

AC:

AN:

9852

Middle Eastern (MID)

AF:

0.00

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.000374

AC:

AN:

66914

Other (OTH)

AF:

0.00

AC:

AN:

2048

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.00

Hom.:

299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.21

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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2-210298339-TACACACACACACAC-TACACACAC

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