NM_079420.3:c.304+75_304+80dupGTGTGT

Variant names:

• chr2-210298339-T-TACACAC
• rs112894708
• NM_079420.3:c.304+75_304+80dupGTGTGT

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+75_304+80dupGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,175,300 control chromosomes in the GnomAD database, including 4,098 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.16 (1852 hom., cov: 0)
  • Exomes 𝑓: 0.16 (2246 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-TACACAC is Benign according to our data. Variant chr2-210298339-T-TACACAC is described in ClinVar as Benign. ClinVar VariationId is 1244285.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 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+75_304+80dupGTGTGT		intron	N/A	NP_524144.1	P05976-1
	MYL1	NM_079422.3		c.172+75_172+80dupGTGTGT		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+81insGTGTGT		intron	N/A	ENSP00000307280.4	P05976-1
	MYL1	ENST00000341685.8	TSL:1	c.172+80_172+81insGTGTGT		intron	N/A	ENSP00000343321.4	P05976-2
	MYL1	ENST00000957378.1		c.268+80_268+81insGTGTGT		intron	N/A	ENSP00000627437.1

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23235 AN: 147138 Hom.: 1855 Cov.: 0

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.188

GnomAD4 exome AF: 0.157 AC: 160923 AN: 1028054 Hom.: 2246 AF XY: 0.158 AC XY: 82923 AN XY: 524086

African (AFR) AF: 0.0972 AC: 2542 AN: 26150

American (AMR) AF: 0.205 AC: 8386 AN: 40990

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 4660 AN: 20946

East Asian (EAS) AF: 0.151 AC: 5296 AN: 34976

South Asian (SAS) AF: 0.183 AC: 12926 AN: 70800

European-Finnish (FIN) AF: 0.146 AC: 6436 AN: 44032

Middle Eastern (MID) AF: 0.270 AC: 1053 AN: 3896

European-Non Finnish (NFE) AF: 0.151 AC: 112243 AN: 741008

Other (OTH) AF: 0.163 AC: 7381 AN: 45256

GnomAD4 genome AF: 0.158 AC: 23245 AN: 147246 Hom.: 1852 Cov.: 0 AF XY: 0.157 AC XY: 11225 AN XY: 71528

African (AFR) AF: 0.112 AC: 4463 AN: 39826

American (AMR) AF: 0.173 AC: 2537 AN: 14700

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 906 AN: 3428

East Asian (EAS) AF: 0.169 AC: 824 AN: 4880

South Asian (SAS) AF: 0.192 AC: 864 AN: 4510

European-Finnish (FIN) AF: 0.143 AC: 1407 AN: 9812

Middle Eastern (MID) AF: 0.339 AC: 97 AN: 286

European-Non Finnish (NFE) AF: 0.175 AC: 11712 AN: 66860

Other (OTH) AF: 0.186 AC: 381 AN: 2048

Alfa AF: 0.112 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 (auto)

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;