chr2-210298339-T-TAC

Position:

• chr2-210298339-T-TAC

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+81insGT 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

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-TAC is Benign according to our data. Variant chr2-210298339-T-TAC is described in ClinVar as [Benign]. Clinvar id 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.

Transcripts

RefSeq

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

Ensembl

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

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

Gnomad4 AFR exome AF: 0.108

Gnomad4 AMR exome AF: 0.0196

Gnomad4 ASJ exome AF: 0.0126

Gnomad4 EAS exome AF: 0.00763

Gnomad4 SAS exome AF: 0.0543

Gnomad4 FIN exome AF: 0.0210

Gnomad4 NFE exome AF: 0.0184

Gnomad4 OTH exome AF: 0.0272

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

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.0242

Gnomad4 ASJ AF: 0.0146

Gnomad4 EAS AF: 0.0127

Gnomad4 SAS AF: 0.0678

Gnomad4 FIN AF: 0.0201

Gnomad4 NFE AF: 0.0214

Gnomad4 OTH AF: 0.0488

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 20, 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;