2-210298339-T-TACACACAC

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+81insGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 1,179,084 control chromosomes in the GnomAD database, including 3,405 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.15 (1769 hom., cov: 0)
  • Exomes 𝑓: 0.13 (1636 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-TACACACAC is Benign according to our data. Variant chr2-210298339-T-TACACACAC is described in ClinVar as [Benign]. Clinvar id is 1253918.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21339 AN: 147152 Hom.: 1766 Cov.: 0

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.110

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.152

GnomAD4 exome AF: 0.128 AC: 132537 AN: 1031824 Hom.: 1636 AF XY: 0.128 AC XY: 67252 AN XY: 525956

Gnomad4 AFR exome AF: 0.0539

Gnomad4 AMR exome AF: 0.242

Gnomad4 ASJ exome AF: 0.0996

Gnomad4 EAS exome AF: 0.200

Gnomad4 SAS exome AF: 0.118

Gnomad4 FIN exome AF: 0.163

Gnomad4 NFE exome AF: 0.121

Gnomad4 OTH exome AF: 0.128

GnomAD4 genome AF: 0.145 AC: 21357 AN: 147260 Hom.: 1769 Cov.: 0 AF XY: 0.150 AC XY: 10705 AN XY: 71556

Gnomad4 AFR AF: 0.0680

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.156

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 14, 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;