rs4524871

Variant names:

• chr9-110700728-G-C
• rs4524871
• NM_005592.4:c.628+3262G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005592.4(MUSK):​c.628+3262G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,100 control chromosomes in the GnomAD database, including 1,820 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 0.14 (1820 hom., cov: 32)
• Consequence: MUSK NM_005592.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667
• Publications: 5 publications found

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]

MUSK Gene-Disease associations (from GenCC):

• congenital myasthenic syndrome 9

  Inheritance: AR Classification: STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), PanelApp Australia
• fetal akinesia deformation sequence 1

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
• postsynaptic congenital myasthenic syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005592.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUSK	NM_005592.4	MANE Select	c.628+3262G>C		intron	N/A	NP_005583.1
	MUSK	NM_001166280.2		c.628+3262G>C		intron	N/A	NP_001159752.1
	MUSK	NM_001166281.2		c.628+3262G>C		intron	N/A	NP_001159753.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUSK	ENST00000374448.9	TSL:5 MANE Select	c.628+3262G>C		intron	N/A	ENSP00000363571.4
	MUSK	ENST00000416899.7	TSL:5	c.628+3262G>C		intron	N/A	ENSP00000393608.3
	MUSK	ENST00000189978.10	TSL:5	c.628+3262G>C		intron	N/A	ENSP00000189978.6

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21129 AN: 151982 Hom.: 1814 Cov.: 32

Gnomad AFR AF: 0.0414

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.0922

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.139 AC: 21140 AN: 152100 Hom.: 1820 Cov.: 32 AF XY: 0.143 AC XY: 10619 AN XY: 74360

African (AFR) AF: 0.0413 AC: 1713 AN: 41510

American (AMR) AF: 0.0920 AC: 1405 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 645 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1026 AN: 5176

South Asian (SAS) AF: 0.189 AC: 912 AN: 4816

European-Finnish (FIN) AF: 0.257 AC: 2713 AN: 10568

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12273 AN: 67970

Other (OTH) AF: 0.116 AC: 244 AN: 2108

Alfa AF: 0.158 Hom.: 258

Bravo AF: 0.121

Asia WGS AF: 0.172 AC: 598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.61
PhyloP100		-0.67
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4524871; hg19: chr9-113463008;