6-2728366-T-C

Position:

• chr6-2728366-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001012418.5(MYLK4):​c.159+20770A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 151,762 control chromosomes in the GnomAD database, including 23,748 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.54 (23748 hom., cov: 31)
• Consequence: MYLK4 NM_001012418.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68

Genes affected

MYLK4 (HGNC:27972): (myosin light chain kinase family member 4) Predicted to enable myosin light chain kinase activity. Predicted to be involved in protein phosphorylation. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

MYLK4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYLK4	NM_001012418.5	c.159+20770A>G		intron_variant		ENST00000274643.9	NP_001012418.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYLK4	ENST00000274643.9	c.159+20770A>G		intron_variant		1	NM_001012418.5	ENSP00000274643.7
MYLK4	ENST00000698899.1	c.327+20770A>G		intron_variant				ENSP00000514016.1
MYLK4	ENST00000647417.1	c.141+15530A>G		intron_variant				ENSP00000494309.1
MYLK4	ENST00000698900.1	n.420+20770A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82293 AN: 151650 Hom.: 23748 Cov.: 31

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.533

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.542 AC: 82313 AN: 151762 Hom.: 23748 Cov.: 31 AF XY: 0.547 AC XY: 40529 AN XY: 74110

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.537

Alfa AF: 0.603 Hom.: 56542

Bravo AF: 0.533

Asia WGS AF: 0.676 AC: 2349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.075
DANN	Benign	0.57

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: rs4246059; hg19: chr6-2728600;