20-31832151-A-T

Position:

• chr20-31832151-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BP6_Very_Strong

The NM_033118.4(MYLK2):​c.1710+15A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.00069 (0 hom., cov: 32)
  • Exomes 𝑓: 0.037 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MYLK2 NM_033118.4 intron
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0320

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 20-31832151-A-T is Benign according to our data. Variant chr20-31832151-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 1667218.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-31832151-A-T is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYLK2	NM_033118.4	c.1710+15A>T		intron_variant		ENST00000375985.5	NP_149109.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYLK2	ENST00000375985.5	c.1710+15A>T		intron_variant		1	NM_033118.4	ENSP00000365152	P1
MYLK2	ENST00000375994.6	c.1710+15A>T		intron_variant		1		ENSP00000365162	P1
MYLK2	ENST00000468730.1	n.648+15A>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 99 AN: 144160 Hom.: 0 Cov.: 32 FAILED QC

Gnomad AFR AF: 0.000520

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000956

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.00377

Gnomad FIN AF: 0.000871

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000368

Gnomad OTH AF: 0.000494

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0371 AC: 28835 AN: 777568 Hom.: 0 Cov.: 26 AF XY: 0.0351 AC XY: 14179 AN XY: 404050

Gnomad4 AFR exome AF: 0.0334

Gnomad4 AMR exome AF: 0.0141

Gnomad4 ASJ exome AF: 0.0434

Gnomad4 EAS exome AF: 0.0632

Gnomad4 SAS exome AF: 0.00636

Gnomad4 FIN exome AF: 0.0139

Gnomad4 NFE exome AF: 0.0429

Gnomad4 OTH exome AF: 0.0463

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000686 AC: 99 AN: 144322 Hom.: 0 Cov.: 32 AF XY: 0.000896 AC XY: 63 AN XY: 70304

Gnomad4 AFR AF: 0.000543

Gnomad4 AMR AF: 0.000954

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00362

Gnomad4 SAS AF: 0.00376

Gnomad4 FIN AF: 0.000871

Gnomad4 NFE AF: 0.000368

Gnomad4 OTH AF: 0.000488

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

Hypertrophic cardiomyopathy 1 Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 16, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.0010
DANN	Benign	0.39

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: rs6060980; hg19: chr20-30419954;