Genetic Variant TRAPPC11:c.661-3delT (chr4-183675156-CT-C) – ACMG Classification: Benign (-16 pts)

Variant summary

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

The NM_021942.6(TRAPPC11):c.661-3delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 1,474,534 control chromosomes in the GnomAD database, including 9,177 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.094 ( 801 hom., cov: 31)

Exomes 𝑓: 0.11 ( 8376 hom. )

Consequence

TRAPPC11
NM_021942.6 splice_region, intron

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 0.0740

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 4-183675156-CT-C is Benign according to our data. Variant chr4-183675156-CT-C is described in ClinVar as [Benign]. Clinvar id is 261454.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-183675156-CT-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAPPC11	NM_021942.6 link	c.661-3delT		splice_region_variant, intron_variant	Intron 6 of 29	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.661-7delT		splice_region_variant, intron_variant	Intron 6 of 29	1	NM_021942.6	ENSP00000335371.6		Q7Z392-1

Frequencies

GnomAD3 genomes

AF:

0.0936

AC:

14205

AN:

151776

Hom.:

797

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0231

Gnomad AMI

AF:

0.0822

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.0934

Gnomad EAS

AF:

0.124

Gnomad SAS

AF:

0.0883

Gnomad FIN

AF:

0.186

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.113

Gnomad OTH

AF:

0.0920

GnomAD3 exomes

AF:

0.116

AC:

23224

AN:

200328

Hom.:

1505

AF XY:

0.114

AC XY:

12604

AN XY:

110148

show subpopulations

Gnomad AFR exome

AF:

0.0234

Gnomad AMR exome

AF:

0.151

Gnomad ASJ exome

AF:

0.0972

Gnomad EAS exome

AF:

0.129

Gnomad SAS exome

AF:

0.0807

Gnomad FIN exome

AF:

0.184

Gnomad NFE exome

AF:

0.114

Gnomad OTH exome

AF:

0.114

GnomAD4 exome

AF:

0.108

AC:

143326

AN:

1322640

Hom.:

8376

Cov.:

AF XY:

0.108

AC XY:

70950

AN XY:

656782

show subpopulations

Gnomad4 AFR exome

AF:

0.0201

Gnomad4 AMR exome

AF:

0.148

Gnomad4 ASJ exome

AF:

0.0959

Gnomad4 EAS exome

AF:

0.101

Gnomad4 SAS exome

AF:

0.0815

Gnomad4 FIN exome

AF:

0.180

Gnomad4 NFE exome

AF:

0.109

Gnomad4 OTH exome

AF:

0.103

GnomAD4 genome

AF:

0.0936

AC:

14224

AN:

151894

Hom.:

801

Cov.:

AF XY:

0.0970

AC XY:

7199

AN XY:

74220

show subpopulations

Gnomad4 AFR

AF:

0.0230

Gnomad4 AMR

AF:

0.127

Gnomad4 ASJ

AF:

0.0934

Gnomad4 EAS

AF:

0.123

Gnomad4 SAS

AF:

0.0888

Gnomad4 FIN

AF:

0.186

Gnomad4 NFE

AF:

0.113

Gnomad4 OTH

AF:

0.0958

Bravo

AF:

0.0873

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Jul 25, 2018

GeneDx

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

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

4-183675156-CTT-CT

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