2-210303457-T-TC

Position:

• chr2-210303457-T-TC

Variant summary

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

The NM_079420.3(MYL1):​c.133-943_133-942insG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 1,336,116 control chromosomes in the GnomAD database, including 100,904 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.41 (12588 hom., cov: 0)
  • Exomes 𝑓: 0.38 (88316 hom.)
• Consequence: MYL1 NM_079420.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.257

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 2-210303457-T-TC is Benign according to our data. Variant chr2-210303457-T-TC is described in ClinVar as [Benign]. Clinvar id is 1221134.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYL1	NM_079420.3	c.133-943_133-942insG		intron_variant		ENST00000352451.4
MYL1	NM_079422.3	c.3+84_3+85insG		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYL1	ENST00000352451.4	c.133-943_133-942insG		intron_variant		1	NM_079420.3
MYL1	ENST00000341685.8	c.3+84_3+85insG		intron_variant		1		P1
MYL1	ENST00000484290.1	n.74+84_74+85insG		intron_variant, non_coding_transcript_variant		5
MYL1	ENST00000496436.5	n.74+84_74+85insG		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61511 AN: 151826 Hom.: 12546 Cov.: 0

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.419

GnomAD4 exome AF: 0.377 AC: 446420 AN: 1184172 Hom.: 88316 AF XY: 0.379 AC XY: 225998 AN XY: 596224

Gnomad4 AFR exome AF: 0.387

Gnomad4 AMR exome AF: 0.561

Gnomad4 ASJ exome AF: 0.428

Gnomad4 EAS exome AF: 0.441

Gnomad4 SAS exome AF: 0.456

Gnomad4 FIN exome AF: 0.447

Gnomad4 NFE exome AF: 0.353

Gnomad4 OTH exome AF: 0.393

GnomAD4 genome AF: 0.406 AC: 61616 AN: 151944 Hom.: 12588 Cov.: 0 AF XY: 0.414 AC XY: 30754 AN XY: 74264

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.419

Alfa AF: 0.389 Hom.: 1431

Bravo AF: 0.405

Asia WGS AF: 0.497 AC: 1725 AN: 3478

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 13, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs35179660; hg19: chr2-211168181;