2-210302408-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_079420.3(MYL1):c.160+80T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 1,347,298 control chromosomes in the GnomAD database, including 102,204 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.41 (12604 hom., cov: 32)
  • Exomes 𝑓: 0.38 (89600 hom.)
• Consequence: MYL1 NM_079420.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.452

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BP6: Variant 2-210302408-A-T is Benign according to our data. Variant chr2-210302408-A-T is described in ClinVar as [Benign]. Clinvar id is 1294855.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.160+80T>A		intron_variant		ENST00000352451.4
MYL1	NM_079422.3	c.28+360T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYL1	ENST00000352451.4	c.160+80T>A		intron_variant		1	NM_079420.3
MYL1	ENST00000341685.8	c.28+360T>A		intron_variant		1		P1
MYL1	ENST00000484290.1	n.291+80T>A		intron_variant, non_coding_transcript_variant		5
MYL1	ENST00000496436.5	n.263+360T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61577 AN: 151802 Hom.: 12563 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.417

GnomAD4 exome AF: 0.383 AC: 458084 AN: 1195378 Hom.: 89600 AF XY: 0.385 AC XY: 229880 AN XY: 597512

Gnomad4 AFR exome AF: 0.391

Gnomad4 AMR exome AF: 0.551

Gnomad4 ASJ exome AF: 0.431

Gnomad4 EAS exome AF: 0.441

Gnomad4 SAS exome AF: 0.456

Gnomad4 FIN exome AF: 0.448

Gnomad4 NFE exome AF: 0.364

Gnomad4 OTH exome AF: 0.399

GnomAD4 genome AF: 0.406 AC: 61681 AN: 151920 Hom.: 12604 Cov.: 32 AF XY: 0.415 AC XY: 30794 AN XY: 74278

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.418

Alfa AF: 0.390 Hom.: 1465

Bravo AF: 0.406

Asia WGS AF: 0.498 AC: 1728 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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	14
Dann	Benign	0.73

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: rs2292300; hg19: chr2-211167132;