chr9-110705266-T-C

Position:

• chr9-110705266-T-C

Variant summary

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

The NM_005592.4(MUSK):​c.628+7800T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 152,000 control chromosomes in the GnomAD database, including 17,606 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 0.47 (17606 hom., cov: 32)
• Consequence: MUSK NM_005592.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354

Genes affected

MUSK (HGNC:7525): (muscle associated receptor tyrosine kinase) This gene encodes a muscle-specific tyrosine kinase receptor. The encoded protein may play a role in clustering of the acetylcholine receptor in the postsynaptic neuromuscular junction. Mutations in this gene have been associated with congenital myasthenic syndrome. Alternatively spliced transcript variants have been described.[provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUSK	NM_005592.4	c.628+7800T>C		intron_variant		ENST00000374448.9	NP_005583.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUSK	ENST00000374448.9	c.628+7800T>C		intron_variant		5	NM_005592.4	ENSP00000363571	P4
MUSK	ENST00000189978.10	c.628+7800T>C		intron_variant		5		ENSP00000189978
MUSK	ENST00000374439.1	c.323-810T>C		intron_variant		5		ENSP00000363562
MUSK	ENST00000416899.7	c.628+7800T>C		intron_variant		5		ENSP00000393608	A1

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71685 AN: 151880 Hom.: 17596 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.472 AC: 71748 AN: 152000 Hom.: 17606 Cov.: 32 AF XY: 0.474 AC XY: 35240 AN XY: 74272

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.449

Alfa AF: 0.406 Hom.: 16952

Bravo AF: 0.471

Asia WGS AF: 0.590 AC: 2051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.4
DANN	Benign	0.78

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: rs7856889; hg19: chr9-113467546;