rs113604435

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000505676.5(TRAPPC11):n.-6G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0366 in 1,600,768 control chromosomes in the GnomAD database, including 1,425 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.056 ( 300 hom., cov: 31)

Exomes 𝑓: 0.035 ( 1125 hom. )

Consequence

TRAPPC11
ENST00000505676.5 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.0560

Publications

6 publications found

Variant links:

Genes affected

TRAPPC11 (HGNC:25751): (trafficking protein particle complex subunit 11) The protein encoded by this gene is a subunit of the TRAPP (transport protein particle) tethering complex, which functions in intracellular vesicle trafficking. This subunit is involved in early stage endoplasmic reticulum-to-Golgi vesicle transport. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2013]

TRAPPC11 Gene-Disease associations (from GenCC):

autosomal recessive limb-girdle muscular dystrophy
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
autosomal recessive limb-girdle muscular dystrophy type R18
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Myriad Women’s Health, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, G2P, Orphanet
intellectual disability-hyperkinetic movement-truncal ataxia syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
triple-A syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

TRAPPC11 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 4-183663862-G-A is Benign according to our data. Variant chr4-183663862-G-A is described in ClinVar as Benign. ClinVar VariationId is 261440.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAPPC11	NM_021942.6 link	c.-6G>A		5_prime_UTR_variant	Exon 2 of 30	ENST00000334690.11	NP_068761.4	Q7Z392-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRAPPC11	ENST00000334690.11 link	c.-6G>A		5_prime_UTR_variant	Exon 2 of 30	1	NM_021942.6	ENSP00000335371.6		Q7Z392-1

Frequencies

GnomAD3 genomes

AF:

0.0556

AC:

8386

AN:

150932

Hom.:

297

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0988

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.0446

Gnomad ASJ

AF:

0.0312

Gnomad EAS

AF:

0.000196

Gnomad SAS

AF:

0.00670

Gnomad FIN

AF:

0.0887

Gnomad MID

AF:

0.0541

Gnomad NFE

AF:

0.0365

Gnomad OTH

AF:

0.0491

GnomAD2 exomes

AF:

0.0365

AC:

9137

AN:

250512

AF XY:

0.0344

show subpopulations

Gnomad AFR exome

AF:

0.100

Gnomad AMR exome

AF:

0.0271

Gnomad ASJ exome

AF:

0.0313

Gnomad EAS exome

AF:

0.000163

Gnomad FIN exome

AF:

0.0792

Gnomad NFE exome

AF:

0.0361

Gnomad OTH exome

AF:

0.0379

GnomAD4 exome

AF:

0.0346

AC:

50203

AN:

1449720

Hom.:

1125

Cov.:

AF XY:

0.0337

AC XY:

24302

AN XY:

721132

show subpopulations

African (AFR)

AF:

0.103

AC:

3405

AN:

32992

American (AMR)

AF:

0.0282

AC:

1242

AN:

44022

Ashkenazi Jewish (ASJ)

AF:

0.0307

AC:

785

AN:

25594

East Asian (EAS)

AF:

0.000128

AC:

AN:

39092

South Asian (SAS)

AF:

0.00743

AC:

639

AN:

86028

European-Finnish (FIN)

AF:

0.0804

AC:

4244

AN:

52814

Middle Eastern (MID)

AF:

0.0380

AC:

215

AN:

5656

European-Non Finnish (NFE)

AF:

0.0340

AC:

37482

AN:

1103950

Other (OTH)

AF:

0.0367

AC:

2186

AN:

59572

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

2149

4297

6446

8594

10743

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1408

2816

4224

5632

7040

<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:

0.0557

AC:

8416

AN:

151048

Hom.:

300

Cov.:

AF XY:

0.0578

AC XY:

4262

AN XY:

73728

show subpopulations

African (AFR)

AF:

0.0992

AC:

4079

AN:

41124

American (AMR)

AF:

0.0445

AC:

672

AN:

15086

Ashkenazi Jewish (ASJ)

AF:

0.0312

AC:

108

AN:

3466

East Asian (EAS)

AF:

0.000197

AC:

AN:

5082

South Asian (SAS)

AF:

0.00671

AC:

AN:

4770

European-Finnish (FIN)

AF:

0.0887

AC:

917

AN:

10342

Middle Eastern (MID)

AF:

0.0586

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.0365

AC:

2476

AN:

67878

Other (OTH)

AF:

0.0491

AC:

103

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

396

792

1187

1583

1979

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

264

352

440

<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:

0.0386

Hom.:

284

Bravo

AF:

0.0529

Asia WGS

AF:

0.0230

AC:

AN:

3478

EpiCase

AF:

0.0363

EpiControl

AF:

0.0353

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Aug 17, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.6

(source)

DANN

Benign

0.81

PhyloP100

0.056

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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