Variant chr20-31819317-AC-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The ENST00000375994.6(MYLK2):c.-260del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0057 in 527,948 control chromosomes in the GnomAD database, including 26 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0051 ( 8 hom., cov: 32)

Exomes 𝑓: 0.0059 ( 18 hom. )

Consequence

MYLK2
ENST00000375994.6 5_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.63

Variant links:

Genes affected

MYLK2 (HGNC:16243): (myosin light chain kinase 2) This gene encodes a myosin light chain kinase, a calcium/calmodulin dependent enzyme, that is exclusively expressed in adult skeletal muscle. [provided by RefSeq, Jul 2008]

MYLK2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 20-31819317-AC-A is Benign according to our data. Variant chr20-31819317-AC-A is described in ClinVar as [Likely_benign]. Clinvar id is 1191659.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 779 AD,Digenic gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYLK2	NM_033118.4 linkuse as main transcript			upstream_gene_variant		ENST00000375985.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYLK2	ENST00000375994.6 linkuse as main transcript	c.-260del		5_prime_UTR_variant	1/12	1		P1
MYLK2	ENST00000375985.5 linkuse as main transcript			upstream_gene_variant		1	NM_033118.4	P1

Frequencies

GnomAD3 genomes

AF:

0.00514

AC:

778

AN:

151342

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000827

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00270

Gnomad ASJ

AF:

0.00405

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00315

Gnomad FIN

AF:

0.0151

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00754

Gnomad OTH

AF:

0.00145

GnomAD4 exome

AF:

0.00593

AC:

2232

AN:

376490

Hom.:

Cov.:

AF XY:

0.00585

AC XY:

1177

AN XY:

201180

show subpopulations

Gnomad4 AFR exome

AF:

0.000539

Gnomad4 AMR exome

AF:

0.00181

Gnomad4 ASJ exome

AF:

0.00214

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00410

Gnomad4 FIN exome

AF:

0.0163

Gnomad4 NFE exome

AF:

0.00692

Gnomad4 OTH exome

AF:

0.00530

GnomAD4 genome

AF:

0.00514

AC:

779

AN:

151458

Hom.:

Cov.:

AF XY:

0.00554

AC XY:

410

AN XY:

73994

show subpopulations

Gnomad4 AFR

AF:

0.000824

Gnomad4 AMR

AF:

0.00269

Gnomad4 ASJ

AF:

0.00405

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00315

Gnomad4 FIN

AF:

0.0151

Gnomad4 NFE

AF:

0.00755

Gnomad4 OTH

AF:

0.00144

Alfa

AF:

0.00664

Hom.:

Bravo

AF:

0.00361

Asia WGS

AF:

0.00289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 24, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over