NM_079420.3:c.304+71_304+80dupGTGTGTGTGT

Variant names:

• chr2-210298339-T-TACACACACAC
• rs112894708
• NM_079420.3:c.304+71_304+80dupGTGTGTGTGT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_079420.3(MYL1):​c.304+71_304+80dupGTGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0278 in 1,185,258 control chromosomes in the GnomAD database, including 209 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.030 (101 hom., cov: 0)
  • Exomes 𝑓: 0.027 (108 hom.)
• Consequence: MYL1 NM_079420.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.73
• Publications: 0 publications found

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

ENSG00000279317 (HGNC:):

ACMG classification

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

• BP6: Variant 2-210298339-T-TACACACACAC is Benign according to our data. Variant chr2-210298339-T-TACACACACAC is described in ClinVar as Benign. ClinVar VariationId is 1270944.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0543 is higher than 0.05.

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+71_304+80dupGTGTGTGTGT		intron	N/A	NP_524144.1	P05976-1
	MYL1	NM_079422.3		c.172+71_172+80dupGTGTGTGTGT		intron	N/A	NP_524146.1	P05976-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYL1	ENST00000352451.4	TSL:1 MANE Select	c.304+80_304+81insGTGTGTGTGT		intron	N/A	ENSP00000307280.4	P05976-1
	MYL1	ENST00000341685.8	TSL:1	c.172+80_172+81insGTGTGTGTGT		intron	N/A	ENSP00000343321.4	P05976-2
	MYL1	ENST00000957378.1		c.268+80_268+81insGTGTGTGTGT		intron	N/A	ENSP00000627437.1

Frequencies

GnomAD3 genomes AF: 0.0304 AC: 4474 AN: 147258 Hom.: 101 Cov.: 0

Gnomad AFR AF: 0.0101

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0542

Gnomad ASJ AF: 0.0443

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.0602

Gnomad FIN AF: 0.0516

Gnomad MID AF: 0.0226

Gnomad NFE AF: 0.0308

Gnomad OTH AF: 0.0247

GnomAD4 exome AF: 0.0275 AC: 28498 AN: 1037892 Hom.: 108 AF XY: 0.0282 AC XY: 14941 AN XY: 528994

African (AFR) AF: 0.00758 AC: 199 AN: 26270

American (AMR) AF: 0.0427 AC: 1794 AN: 42022

Ashkenazi Jewish (ASJ) AF: 0.0354 AC: 748 AN: 21150

East Asian (EAS) AF: 0.0463 AC: 1646 AN: 35558

South Asian (SAS) AF: 0.0471 AC: 3362 AN: 71368

European-Finnish (FIN) AF: 0.0432 AC: 1922 AN: 44518

Middle Eastern (MID) AF: 0.0139 AC: 55 AN: 3952

European-Non Finnish (NFE) AF: 0.0235 AC: 17591 AN: 747278

Other (OTH) AF: 0.0258 AC: 1181 AN: 45776

GnomAD4 genome AF: 0.0304 AC: 4479 AN: 147366 Hom.: 101 Cov.: 0 AF XY: 0.0328 AC XY: 2345 AN XY: 71594

African (AFR) AF: 0.0100 AC: 400 AN: 39852

American (AMR) AF: 0.0543 AC: 798 AN: 14708

Ashkenazi Jewish (ASJ) AF: 0.0443 AC: 152 AN: 3430

East Asian (EAS) AF: 0.0471 AC: 230 AN: 4880

South Asian (SAS) AF: 0.0602 AC: 272 AN: 4518

European-Finnish (FIN) AF: 0.0516 AC: 508 AN: 9850

Middle Eastern (MID) AF: 0.0208 AC: 6 AN: 288

European-Non Finnish (NFE) AF: 0.0308 AC: 2062 AN: 66896

Other (OTH) AF: 0.0249 AC: 51 AN: 2048

Alfa AF: 0.0294 Hom.: 299

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs112894708; hg19: chr2-211163063;