NM_079420.3:c.304+79_304+80delGT

Variant names:

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

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+80delGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 1,168,034 control chromosomes in the GnomAD database, including 20,643 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.28 (6224 hom., cov: 0)
  • Exomes 𝑓: 0.32 (14419 hom.)
• Consequence: MYL1 NM_079420.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.189
• 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-TAC-T is Benign according to our data. Variant chr2-210298339-TAC-T is described in ClinVar as Benign. ClinVar VariationId is 1286878.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.35 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+80delGT		intron	N/A	NP_524144.1	P05976-1
	MYL1	NM_079422.3		c.172+79_172+80delGT		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+79_304+80delGT		intron	N/A	ENSP00000307280.4	P05976-1
	MYL1	ENST00000341685.8	TSL:1	c.172+79_172+80delGT		intron	N/A	ENSP00000343321.4	P05976-2
	MYL1	ENST00000957378.1		c.268+79_268+80delGT		intron	N/A	ENSP00000627437.1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 40892 AN: 147120 Hom.: 6222 Cov.: 0

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.279

GnomAD4 exome AF: 0.317 AC: 323475 AN: 1020812 Hom.: 14419 AF XY: 0.315 AC XY: 163778 AN XY: 519942

African (AFR) AF: 0.186 AC: 4560 AN: 24506

American (AMR) AF: 0.241 AC: 10036 AN: 41640

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 5455 AN: 20638

East Asian (EAS) AF: 0.238 AC: 8213 AN: 34480

South Asian (SAS) AF: 0.274 AC: 19222 AN: 70276

European-Finnish (FIN) AF: 0.337 AC: 14879 AN: 44146

Middle Eastern (MID) AF: 0.220 AC: 858 AN: 3898

European-Non Finnish (NFE) AF: 0.335 AC: 246869 AN: 736376

Other (OTH) AF: 0.298 AC: 13383 AN: 44852

GnomAD4 genome AF: 0.278 AC: 40895 AN: 147222 Hom.: 6224 Cov.: 0 AF XY: 0.277 AC XY: 19795 AN XY: 71522

African (AFR) AF: 0.138 AC: 5493 AN: 39816

American (AMR) AF: 0.265 AC: 3895 AN: 14704

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 800 AN: 3430

East Asian (EAS) AF: 0.242 AC: 1179 AN: 4878

South Asian (SAS) AF: 0.275 AC: 1238 AN: 4506

European-Finnish (FIN) AF: 0.377 AC: 3711 AN: 9836

Middle Eastern (MID) AF: 0.204 AC: 58 AN: 284

European-Non Finnish (NFE) AF: 0.354 AC: 23667 AN: 66828

Other (OTH) AF: 0.280 AC: 572 AN: 2046

Alfa AF: 0.271 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		0.19
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs112894708; hg19: chr2-211163063;