chr2-210298339-T-TAC

Variant names:

• chr2-210298339-T-TAC
• rs112894708
• NM_079420.3:c.304+79_304+80dupGT

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+79_304+80dupGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0266 in 1,183,698 control chromosomes in the GnomAD database, including 374 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.051 (330 hom., cov: 0)
  • Exomes 𝑓: 0.023 (44 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-TAC is Benign according to our data. Variant chr2-210298339-T-TAC is described in ClinVar as Benign. ClinVar VariationId is 1277854.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 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+79_304+80dupGT		intron	N/A	NP_524144.1	P05976-1
	MYL1	NM_079422.3		c.172+79_172+80dupGT		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+81insGT		intron	N/A	ENSP00000307280.4	P05976-1
	MYL1	ENST00000341685.8	TSL:1	c.172+80_172+81insGT		intron	N/A	ENSP00000343321.4	P05976-2
	MYL1	ENST00000957378.1		c.268+80_268+81insGT		intron	N/A	ENSP00000627437.1

Frequencies

GnomAD3 genomes AF: 0.0507 AC: 7470 AN: 147256 Hom.: 331 Cov.: 0

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0123

Gnomad AMR AF: 0.0243

Gnomad ASJ AF: 0.0146

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.0201

Gnomad MID AF: 0.0226

Gnomad NFE AF: 0.0214

Gnomad OTH AF: 0.0494

GnomAD4 exome AF: 0.0232 AC: 24040 AN: 1036334 Hom.: 44 AF XY: 0.0242 AC XY: 12797 AN XY: 528268

African (AFR) AF: 0.108 AC: 2813 AN: 26128

American (AMR) AF: 0.0196 AC: 824 AN: 42088

Ashkenazi Jewish (ASJ) AF: 0.0126 AC: 265 AN: 21086

East Asian (EAS) AF: 0.00763 AC: 272 AN: 35666

South Asian (SAS) AF: 0.0543 AC: 3871 AN: 71298

European-Finnish (FIN) AF: 0.0210 AC: 934 AN: 44538

Middle Eastern (MID) AF: 0.0262 AC: 103 AN: 3928

European-Non Finnish (NFE) AF: 0.0184 AC: 13715 AN: 745938

Other (OTH) AF: 0.0272 AC: 1243 AN: 45664

GnomAD4 genome AF: 0.0507 AC: 7478 AN: 147364 Hom.: 330 Cov.: 0 AF XY: 0.0516 AC XY: 3692 AN XY: 71606

African (AFR) AF: 0.124 AC: 4956 AN: 39824

American (AMR) AF: 0.0242 AC: 356 AN: 14724

Ashkenazi Jewish (ASJ) AF: 0.0146 AC: 50 AN: 3430

East Asian (EAS) AF: 0.0127 AC: 62 AN: 4882

South Asian (SAS) AF: 0.0678 AC: 306 AN: 4516

European-Finnish (FIN) AF: 0.0201 AC: 198 AN: 9854

Middle Eastern (MID) AF: 0.0243 AC: 7 AN: 288

European-Non Finnish (NFE) AF: 0.0214 AC: 1432 AN: 66902

Other (OTH) AF: 0.0488 AC: 100 AN: 2048

Alfa AF: 0.0217 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;