Variant 11-119019100-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_016146.6(TRAPPC4):c.176-43C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0949 in 1,600,800 control chromosomes in the GnomAD database, including 8,437 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.085 ( 655 hom., cov: 32)

Exomes 𝑓: 0.096 ( 7782 hom. )

Consequence

TRAPPC4
NM_016146.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0320

Variant links:

Genes affected

TRAPPC4 (HGNC:19943): (trafficking protein particle complex subunit 4) Involved in autophagy and endoplasmic reticulum to Golgi vesicle-mediated transport. Part of TRAPP complex. [provided by Alliance of Genome Resources, Apr 2022]

TRAPPC4 links:

TRAPPC4 (HGNC:):

TRAPPC4 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 (BayesDel_noAF=-0.65).

BP6

Variant 11-119019100-C-T is Benign according to our data. Variant chr11-119019100-C-T is described in ClinVar as [Benign]. Clinvar id is 1182463.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRAPPC4	NM_016146.6 linkuse as main transcript	c.176-43C>T		intron_variant		ENST00000533632.6	NP_057230.1	Q9Y296-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRAPPC4	ENST00000533632.6 linkuse as main transcript	c.176-43C>T		intron_variant		1	NM_016146.6	ENSP00000436005.1		Q9Y296-1

Frequencies

GnomAD3 genomes

AF:

0.0847

AC:

12872

AN:

152034

Hom.:

653

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0696

Gnomad AMI

AF:

0.0976

Gnomad AMR

AF:

0.0583

Gnomad ASJ

AF:

0.0325

Gnomad EAS

AF:

0.0788

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.144

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0835

Gnomad OTH

AF:

0.0657

GnomAD3 exomes

AF:

0.0990

AC:

24032

AN:

242696

Hom.:

1469

AF XY:

0.107

AC XY:

14000

AN XY:

131268

show subpopulations

Gnomad AFR exome

AF:

0.0707

Gnomad AMR exome

AF:

0.0616

Gnomad ASJ exome

AF:

0.0402

Gnomad EAS exome

AF:

0.0785

Gnomad SAS exome

AF:

0.221

Gnomad FIN exome

AF:

0.141

Gnomad NFE exome

AF:

0.0834

Gnomad OTH exome

AF:

0.0768

GnomAD4 exome

AF:

0.0960

AC:

139060

AN:

1448648

Hom.:

7782

Cov.:

AF XY:

0.0997

AC XY:

71625

AN XY:

718636

show subpopulations

Gnomad4 AFR exome

AF:

0.0669

Gnomad4 AMR exome

AF:

0.0619

Gnomad4 ASJ exome

AF:

0.0398

Gnomad4 EAS exome

AF:

0.0956

Gnomad4 SAS exome

AF:

0.221

Gnomad4 FIN exome

AF:

0.137

Gnomad4 NFE exome

AF:

0.0882

Gnomad4 OTH exome

AF:

0.0917

GnomAD4 genome

AF:

0.0847

AC:

12884

AN:

152152

Hom.:

655

Cov.:

AF XY:

0.0889

AC XY:

6610

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.0696

Gnomad4 AMR

AF:

0.0582

Gnomad4 ASJ

AF:

0.0325

Gnomad4 EAS

AF:

0.0790

Gnomad4 SAS

AF:

0.233

Gnomad4 FIN

AF:

0.144

Gnomad4 NFE

AF:

0.0835

Gnomad4 OTH

AF:

0.0697

Alfa

AF:

0.0786

Hom.:

141

Bravo

AF:

0.0740

Asia WGS

AF:

0.161

AC:

560

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 15, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

7.8

DANN

Benign

0.85

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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