rs34729771

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_005055.5(RAPSN):c.691-11delC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.61 ( 30441 hom., cov: 0)

Exomes 𝑓: 0.70 ( 351164 hom. )

Consequence

RAPSN
NM_005055.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: -0.0750

Publications

8 publications found

Variant links:

Genes affected

RAPSN (HGNC:9863): (receptor associated protein of the synapse) This gene encodes a member of a family of proteins that are receptor associated proteins of the synapse. The encoded protein contains a conserved cAMP-dependent protein kinase phosphorylation site, and plays a critical role in clustering and anchoring nicotinic acetylcholine receptors at synaptic sites by linking the receptors to the underlying postsynaptic cytoskeleton, possibly by direct association with actin or spectrin. Mutations in this gene may play a role in postsynaptic congenital myasthenic syndromes. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Apr 2011]

RAPSN Gene-Disease associations (from GenCC):

fetal akinesia deformation sequence 2
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
neuromuscular disease
Inheritance: AR Classification: DEFINITIVE Submitted by: Ambry Genetics
congenital myasthenic syndrome 11
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Genomics England PanelApp
fetal akinesia deformation sequence 1
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
postsynaptic congenital myasthenic syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

RAPSN links:

LOC124902673 (HGNC:):

LOC124902673 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP6

Variant 11-47441931-AG-A is Benign according to our data. Variant chr11-47441931-AG-A is described in ClinVar as Benign. ClinVar VariationId is 197249.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAPSN	NM_005055.5 link	c.691-11delC		intron_variant	Intron 3 of 7	ENST00000298854.7	NP_005046.2	Q13702-1A0A0S2Z4F8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAPSN	ENST00000298854.7 link	c.691-11delC		intron_variant	Intron 3 of 7	1	NM_005055.5	ENSP00000298854.2		Q13702-1

Frequencies

GnomAD3 genomes

AF:

0.614

AC:

93335

AN:

152042

Hom.:

30426

Cov.:

show subpopulations

Gnomad AFR

AF:

0.381

Gnomad AMI

AF:

0.868

Gnomad AMR

AF:

0.663

Gnomad ASJ

AF:

0.716

Gnomad EAS

AF:

0.659

Gnomad SAS

AF:

0.786

Gnomad FIN

AF:

0.606

Gnomad MID

AF:

0.715

Gnomad NFE

AF:

0.720

Gnomad OTH

AF:

0.673

GnomAD2 exomes

AF:

0.679

AC:

114250

AN:

168348

AF XY:

0.693

show subpopulations

Gnomad AFR exome

AF:

0.378

Gnomad AMR exome

AF:

0.618

Gnomad ASJ exome

AF:

0.723

Gnomad EAS exome

AF:

0.642

Gnomad FIN exome

AF:

0.605

Gnomad NFE exome

AF:

0.722

Gnomad OTH exome

AF:

0.724

GnomAD4 exome

AF:

0.703

AC:

989419

AN:

1407860

Hom.:

351164

Cov.:

AF XY:

0.706

AC XY:

491770

AN XY:

696436

show subpopulations

African (AFR)

AF:

0.372

AC:

12221

AN:

32854

American (AMR)

AF:

0.626

AC:

23277

AN:

37186

Ashkenazi Jewish (ASJ)

AF:

0.720

AC:

18181

AN:

25262

East Asian (EAS)

AF:

0.596

AC:

22653

AN:

37980

South Asian (SAS)

AF:

0.769

AC:

61864

AN:

80442

European-Finnish (FIN)

AF:

0.618

AC:

26090

AN:

42222

Middle Eastern (MID)

AF:

0.738

AC:

3014

AN:

4082

European-Non Finnish (NFE)

AF:

0.717

AC:

780855

AN:

1089296

Other (OTH)

AF:

0.705

AC:

41264

AN:

58536

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

18011

36022

54034

72045

90056

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19538

39076

58614

78152

97690

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.614

AC:

93390

AN:

152160

Hom.:

30441

Cov.:

AF XY:

0.613

AC XY:

45596

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.381

AC:

15800

AN:

41492

American (AMR)

AF:

0.663

AC:

10148

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.716

AC:

2486

AN:

3472

East Asian (EAS)

AF:

0.658

AC:

3399

AN:

5166

South Asian (SAS)

AF:

0.784

AC:

3785

AN:

4826

European-Finnish (FIN)

AF:

0.606

AC:

6423

AN:

10604

Middle Eastern (MID)

AF:

0.721

AC:

212

AN:

294

European-Non Finnish (NFE)

AF:

0.720

AC:

48917

AN:

67986

Other (OTH)

AF:

0.677

AC:

1432

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1742

3485

5227

6970

8712

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

762

1524

2286

3048

3810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.686

Hom.:

6621

Bravo

AF:

0.604

Asia WGS

AF:

0.720

AC:

2505

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

May 21, 2015

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Congenital Myasthenic Syndrome, Recessive

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Fetal akinesia deformation sequence 1

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

May 31, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Fetal akinesia deformation sequence 1;C4225367:Congenital myasthenic syndrome 11

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Fetal akinesia deformation sequence 2

Benign:1

Nov 07, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Congenital myasthenic syndrome

Benign:1

Sep 16, 2020

Natera, Inc.

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Congenital myasthenic syndrome 11

Benign:1

Nov 07, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.075

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over