Genetic Variant TRAPPC11:c.-21-97_-21-92delTTTTTT (chr4-183663736-GTTTTTT-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_021942.6(TRAPPC11):c.-21-97_-21-92delTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000093 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

TRAPPC11
NM_021942.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.972

Publications

0 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: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), G2P, Myriad Women’s Health, 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: Uncertain_significance. The variant received 0 ACMG points.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRAPPC11	NM_021942.6	MANE Select	c.-21-97_-21-92delTTTTTT		intron	N/A	NP_068761.4
	TRAPPC11	NM_199053.3		c.-21-97_-21-92delTTTTTT		intron	N/A	NP_951008.1	Q7Z392-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TRAPPC11	ENST00000334690.11	TSL:1 MANE Select	c.-21-110_-21-105delTTTTTT	intron	N/A	ENSP00000335371.6	Q7Z392-1
TRAPPC11	ENST00000357207.8	TSL:1	c.-21-110_-21-105delTTTTTT	intron	N/A	ENSP00000349738.4	Q7Z392-3
TRAPPC11	ENST00000505676.5	TSL:1	n.-21-110_-21-105delTTTTTT	intron	N/A	ENSP00000422915.1	D6R9T9

Frequencies

GnomAD3 genomes

AF:

0.00000925

AC:

AN:

108062

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000195

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

280248

Hom.:

AF XY:

0.00

AC XY:

AN XY:

147216

African (AFR)

AF:

0.00

AC:

AN:

7138

American (AMR)

AF:

0.00

AC:

AN:

11156

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

8200

East Asian (EAS)

AF:

0.00

AC:

AN:

17882

South Asian (SAS)

AF:

0.00

AC:

AN:

27092

European-Finnish (FIN)

AF:

0.00

AC:

AN:

20358

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1156

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

171382

Other (OTH)

AF:

0.00

AC:

AN:

15884

GnomAD4 genome

AF:

0.00000925

AC:

AN:

108062

Hom.:

Cov.:

AF XY:

0.0000196

AC XY:

AN XY:

51066

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

29512

American (AMR)

AF:

0.00

AC:

AN:

10592

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2834

East Asian (EAS)

AF:

0.00

AC:

AN:

3444

South Asian (SAS)

AF:

0.00

AC:

AN:

3232

European-Finnish (FIN)

AF:

0.00

AC:

AN:

4686

Middle Eastern (MID)

AF:

0.00

AC:

AN:

216

European-Non Finnish (NFE)

AF:

0.0000195

AC:

AN:

51308

Other (OTH)

AF:

0.00

AC:

AN:

1466

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.825

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.97

Splicing

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.

4-183663736-GTTTTTTTT-GTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over