Variant chr9-110762231-AT-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_005592.4(MUSK):c.920+25delT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 13552 hom., cov: 0)

Exomes 𝑓: 0.45 ( 131521 hom. )

Consequence

MUSK
NM_005592.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.00

Variant links:

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 links:

LOC107987115 (HGNC:):

LOC107987115 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 9-110762231-AT-A is Benign according to our data. Variant chr9-110762231-AT-A is described in ClinVar as [Benign]. Clinvar id is 259813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUSK	NM_005592.4 linkuse as main transcript	c.920+25delT		intron_variant		ENST00000374448.9	NP_005583.1	O15146-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
MUSK	ENST00000374448.9 linkuse as main transcript	c.920+25delT	intron_variant	5	NM_005592.4	ENSP00000363571.4	O15146-1
MUSK	ENST00000416899.7 linkuse as main transcript	c.920+25delT	intron_variant	5		ENSP00000393608.3	A0A087WSY1
MUSK	ENST00000189978.10 linkuse as main transcript	c.950+25delT	intron_variant	5		ENSP00000189978.6	O15146-2
MUSK	ENST00000634612.1 linkuse as main transcript	n.342+25delT	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.411

AC:

62325

AN:

151808

Hom.:

13548

Cov.:

show subpopulations

Gnomad AFR

AF:

0.333

Gnomad AMI

AF:

0.597

Gnomad AMR

AF:

0.345

Gnomad ASJ

AF:

0.530

Gnomad EAS

AF:

0.104

Gnomad SAS

AF:

0.312

Gnomad FIN

AF:

0.468

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.484

Gnomad OTH

AF:

0.442

GnomAD3 exomes

AF:

0.387

AC:

64621

AN:

166922

Hom.:

13940

AF XY:

0.395

AC XY:

36467

AN XY:

92208

show subpopulations

Gnomad AFR exome

AF:

0.316

Gnomad AMR exome

AF:

0.223

Gnomad ASJ exome

AF:

0.511

Gnomad EAS exome

AF:

0.0961

Gnomad SAS exome

AF:

0.306

Gnomad FIN exome

AF:

0.457

Gnomad NFE exome

AF:

0.478

Gnomad OTH exome

AF:

0.414

GnomAD4 exome

AF:

0.445

AC:

567230

AN:

1273554

Hom.:

131521

Cov.:

AF XY:

0.443

AC XY:

277163

AN XY:

626286

show subpopulations

Gnomad4 AFR exome

AF:

0.314

Gnomad4 AMR exome

AF:

0.242

Gnomad4 ASJ exome

AF:

0.525

Gnomad4 EAS exome

AF:

0.124

Gnomad4 SAS exome

AF:

0.303

Gnomad4 FIN exome

AF:

0.461

Gnomad4 NFE exome

AF:

0.473

Gnomad4 OTH exome

AF:

0.427

GnomAD4 genome

AF:

0.410

AC:

62354

AN:

151926

Hom.:

13552

Cov.:

AF XY:

0.407

AC XY:

30203

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.333

Gnomad4 AMR

AF:

0.345

Gnomad4 ASJ

AF:

0.530

Gnomad4 EAS

AF:

0.104

Gnomad4 SAS

AF:

0.311

Gnomad4 FIN

AF:

0.468

Gnomad4 NFE

AF:

0.484

Gnomad4 OTH

AF:

0.438

Alfa

AF:

0.441

Hom.:

2867

Bravo

AF:

0.396

Asia WGS

AF:

0.203

AC:

709

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Fetal akinesia deformation sequence 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 16, 2018

- -

Congenital myasthenic syndrome 9

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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