2-210298339-T-TACACAC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_079420.3(MYL1):c.304+80_304+81insGTGTGT 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

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]

ACMG classification

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYL1	NM_079420.3	c.304+80_304+81insGTGTGT		intron_variant		ENST00000352451.4
MYL1	NM_079422.3	c.172+80_172+81insGTGTGT		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYL1	ENST00000352451.4	c.304+80_304+81insGTGTGT		intron_variant		1	NM_079420.3
MYL1	ENST00000341685.8	c.172+80_172+81insGTGTGT		intron_variant		1		P1
MYL1	ENST00000484290.1	n.435+80_435+81insGTGTGT		intron_variant, non_coding_transcript_variant		5
MYL1	ENST00000496436.5	n.407+80_407+81insGTGTGT		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR exome AF: 0.0972

Gnomad4 AMR exome AF: 0.205

Gnomad4 ASJ exome AF: 0.222

Gnomad4 EAS exome AF: 0.151

Gnomad4 SAS exome AF: 0.183

Gnomad4 FIN exome AF: 0.146

Gnomad4 NFE exome AF: 0.151

Gnomad4 OTH exome AF: 0.163

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

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.186

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 16, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs112894708; hg19: chr2-211163063;