NM_021942.6:c.145G>C

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_021942.6(TRAPPC11):c.145G>C(p.Val49Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0135 in 1,613,882 control chromosomes in the GnomAD database, including 233 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. V49V) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0099 ( 12 hom., cov: 31)

Exomes 𝑓: 0.014 ( 221 hom. )

Consequence

TRAPPC11
NM_021942.6 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 9.60

Publications

8 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 (MetaRNN=0.0064061284).

BP6

Variant 4-183664012-G-C is Benign according to our data. Variant chr4-183664012-G-C is described in ClinVar as Benign. ClinVar VariationId is 261442.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.00994 (1513/152204) while in subpopulation SAS AF = 0.0402 (194/4824). AF 95% confidence interval is 0.0356. There are 12 homozygotes in GnomAd4. There are 747 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 12 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021942.6. 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
	TRAPPC11	NM_021942.6	MANE Select	c.145G>C	p.Val49Leu	missense	Exon 2 of 30	NP_068761.4
	TRAPPC11	NM_199053.3		c.145G>C	p.Val49Leu	missense	Exon 2 of 31	NP_951008.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
TRAPPC11	ENST00000334690.11	TSL:1 MANE Select	c.145G>C	p.Val49Leu	missense	Exon 2 of 30	ENSP00000335371.6
TRAPPC11	ENST00000357207.8	TSL:1	c.145G>C	p.Val49Leu	missense	Exon 2 of 31	ENSP00000349738.4
TRAPPC11	ENST00000505676.5	TSL:1	n.145G>C		non_coding_transcript_exon	Exon 2 of 19	ENSP00000422915.1

Frequencies

GnomAD3 genomes

AF:

0.00995

AC:

1514

AN:

152086

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00227

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00491

Gnomad ASJ

AF:

0.0196

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.0402

Gnomad FIN

AF:

0.00858

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0141

Gnomad OTH

AF:

0.0105

GnomAD2 exomes

AF:

0.0140

AC:

3510

AN:

251478

AF XY:

0.0160

show subpopulations

Gnomad AFR exome

AF:

0.00172

Gnomad AMR exome

AF:

0.00543

Gnomad ASJ exome

AF:

0.0185

Gnomad EAS exome

AF:

0.00103

Gnomad FIN exome

AF:

0.00975

Gnomad NFE exome

AF:

0.0137

Gnomad OTH exome

AF:

0.0125

GnomAD4 exome

AF:

0.0139

AC:

20268

AN:

1461678

Hom.:

221

Cov.:

AF XY:

0.0149

AC XY:

10832

AN XY:

727138

show subpopulations

African (AFR)

AF:

0.00188

AC:

AN:

33466

American (AMR)

AF:

0.00561

AC:

251

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0182

AC:

475

AN:

26134

East Asian (EAS)

AF:

0.000655

AC:

AN:

39698

South Asian (SAS)

AF:

0.0407

AC:

3512

AN:

86242

European-Finnish (FIN)

AF:

0.00920

AC:

491

AN:

53396

Middle Eastern (MID)

AF:

0.0360

AC:

203

AN:

5636

European-Non Finnish (NFE)

AF:

0.0129

AC:

14381

AN:

1111998

Other (OTH)

AF:

0.0143

AC:

866

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

1112

2224

3337

4449

5561

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

550

1100

1650

2200

2750

<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:

0.00994

AC:

1513

AN:

152204

Hom.:

Cov.:

AF XY:

0.0100

AC XY:

747

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.00226

AC:

AN:

41524

American (AMR)

AF:

0.00490

AC:

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0196

AC:

AN:

3468

East Asian (EAS)

AF:

0.00155

AC:

AN:

5166

South Asian (SAS)

AF:

0.0402

AC:

194

AN:

4824

European-Finnish (FIN)

AF:

0.00858

AC:

AN:

10604

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0141

AC:

956

AN:

68002

Other (OTH)

AF:

0.0104

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

156

235

313

391

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

<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:

0.0134

Hom.:

Bravo

AF:

0.00869

TwinsUK

AF:

0.0138

AC:

ALSPAC

AF:

0.0109

AC:

ESP6500AA

AF:

0.00204

AC:

ESP6500EA

AF:

0.0135

AC:

116

ExAC

AF:

0.0143

AC:

1732

Asia WGS

AF:

0.00924

AC:

AN:

3478

EpiCase

AF:

0.0159

EpiControl

AF:

0.0151

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:6

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

Jun 06, 2019

Athena Diagnostics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Clinical Genetics, Academic Medical Center

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

Aug 27, 2019

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Jul 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

TRAPPC11: BS1, BS2

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Autosomal recessive limb-girdle muscular dystrophy type R18

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.86

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.20

CADD

Uncertain

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.024

Eigen

Uncertain

0.27

Eigen_PC

Uncertain

0.47

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.94

MetaRNN

Benign

0.0064

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.69

PhyloP100

9.6

PrimateAI

Pathogenic

0.81

PROVEAN

Benign

-1.1

REVEL

Benign

0.17

Sift

Benign

0.30

Sift4G

Benign

0.27

Polyphen

0.47

Vest4

0.27

MutPred

0.49

Loss of sheet (P = 0.0181)

MPC

0.21

ClinPred

0.027

GERP RS

6.0

Varity_R

0.15

gMVP

0.62

Mutation Taster

=80/20

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over