rs75176151

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_021942.6(TRAPPC11):c.2483T>C(p.Val828Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00962 in 1,613,952 control chromosomes in the GnomAD database, including 119 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0077 ( 9 hom., cov: 33)

Exomes 𝑓: 0.0098 ( 110 hom. )

Consequence

TRAPPC11
NM_021942.6 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 8.02

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008762926).

BP6

Variant 4-183694013-T-C is Benign according to our data. Variant chr4-183694013-T-C is described in ClinVar as [Benign]. Clinvar id is 261450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-183694013-T-C is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00771 (1174/152340) while in subpopulation NFE AF= 0.0107 (729/68034). AF 95% confidence interval is 0.0101. There are 9 homozygotes in gnomad4. There are 582 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAPPC11	NM_021942.6 link	c.2483T>C	p.Val828Ala	missense_variant	Exon 22 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.2483T>C	p.Val828Ala	missense_variant	Exon 22 of 30	1	NM_021942.6	ENSP00000335371.6		Q7Z392-1

Frequencies

GnomAD3 genomes

AF:

0.00771

AC:

1174

AN:

152222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00215

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.00812

Gnomad ASJ

AF:

0.00605

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00703

Gnomad FIN

AF:

0.0115

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0107

Gnomad OTH

AF:

0.00956

GnomAD3 exomes

AF:

0.00797

AC:

2003

AN:

251238

Hom.:

AF XY:

0.00828

AC XY:

1124

AN XY:

135766

show subpopulations

Gnomad AFR exome

AF:

0.00191

Gnomad AMR exome

AF:

0.00518

Gnomad ASJ exome

AF:

0.00635

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00526

Gnomad FIN exome

AF:

0.00956

Gnomad NFE exome

AF:

0.0116

Gnomad OTH exome

AF:

0.00800

GnomAD4 exome

AF:

0.00982

AC:

14349

AN:

1461612

Hom.:

110

Cov.:

AF XY:

0.00991

AC XY:

7204

AN XY:

727072

show subpopulations

Gnomad4 AFR exome

AF:

0.00188

Gnomad4 AMR exome

AF:

0.00543

Gnomad4 ASJ exome

AF:

0.00750

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00660

Gnomad4 FIN exome

AF:

0.00859

Gnomad4 NFE exome

AF:

0.0110

Gnomad4 OTH exome

AF:

0.00956

GnomAD4 genome

AF:

0.00771

AC:

1174

AN:

152340

Hom.:

Cov.:

AF XY:

0.00781

AC XY:

582

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.00214

Gnomad4 AMR

AF:

0.00811

Gnomad4 ASJ

AF:

0.00605

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00704

Gnomad4 FIN

AF:

0.0115

Gnomad4 NFE

AF:

0.0107

Gnomad4 OTH

AF:

0.00946

Alfa

AF:

0.00995

Hom.:

Bravo

AF:

0.00716

TwinsUK

AF:

0.0119

AC:

ALSPAC

AF:

0.0106

AC:

ESP6500AA

AF:

0.00204

AC:

ESP6500EA

AF:

0.0112

AC:

ExAC

AF:

0.00834

AC:

1013

Asia WGS

AF:

0.00433

AC:

AN:

3478

EpiCase

AF:

0.0117

EpiControl

AF:

0.0113

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Mar 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

TRAPPC11: BP4, BS1, BS2 -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Sep 09, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 28, 2018

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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 v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.44

BayesDel_noAF

Benign

-0.40

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.044

T;.;T

Eigen

Benign

0.17

Eigen_PC

Uncertain

0.27

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.88

D;D;D

MetaRNN

Benign

0.0088

T;T;T

MetaSVM

Benign

-0.79

MutationAssessor

Benign

1.4

L;L;.

PrimateAI

Benign

0.31

PROVEAN

Benign

-1.2

N;N;N

REVEL

Benign

0.076

Sift

Uncertain

0.0090

D;D;D

Sift4G

Benign

0.11

T;T;D

Polyphen

0.17

B;B;P

Vest4

0.56

MVP

0.44

MPC

0.31

ClinPred

0.023

GERP RS

5.8

Varity_R

0.077

gMVP

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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