chr2-210298339-TAC-T

Position:

• chr2-210298339-TAC-T

Variant summary

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

The NM_079420.3(MYL1):​c.304+79_304+80del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 1,168,034 control chromosomes in the GnomAD database, including 20,643 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.28 (6224 hom., cov: 0)
  • Exomes 𝑓: 0.32 (14419 hom.)
• Consequence: MYL1 NM_079420.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.189

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-TAC-T is Benign according to our data. Variant chr2-210298339-TAC-T is described in ClinVar as [Benign]. Clinvar id is 1286878.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYL1	NM_079420.3	c.304+79_304+80del		intron_variant		ENST00000352451.4
MYL1	NM_079422.3	c.172+79_172+80del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYL1	ENST00000352451.4	c.304+79_304+80del		intron_variant		1	NM_079420.3
MYL1	ENST00000341685.8	c.172+79_172+80del		intron_variant		1		P1
MYL1	ENST00000484290.1	n.435+79_435+80del		intron_variant, non_coding_transcript_variant		5
MYL1	ENST00000496436.5	n.407+79_407+80del		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.278 AC: 40892 AN: 147120 Hom.: 6222 Cov.: 0

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.279

GnomAD4 exome AF: 0.317 AC: 323475 AN: 1020812 Hom.: 14419 AF XY: 0.315 AC XY: 163778 AN XY: 519942

Gnomad4 AFR exome AF: 0.186

Gnomad4 AMR exome AF: 0.241

Gnomad4 ASJ exome AF: 0.264

Gnomad4 EAS exome AF: 0.238

Gnomad4 SAS exome AF: 0.274

Gnomad4 FIN exome AF: 0.337

Gnomad4 NFE exome AF: 0.335

Gnomad4 OTH exome AF: 0.298

GnomAD4 genome AF: 0.278 AC: 40895 AN: 147222 Hom.: 6224 Cov.: 0 AF XY: 0.277 AC XY: 19795 AN XY: 71522

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.280

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: rs112894708; hg19: chr2-211163063;