Variant 11-119019312-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_001318486.2(TRAPPC4):c.131C>T(p.Ser44Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0949 in 1,612,310 control chromosomes in the GnomAD database, including 8,540 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/6 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.085 ( 669 hom., cov: 32)

Exomes 𝑓: 0.096 ( 7871 hom. )

Consequence

TRAPPC4
NM_001318486.2 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.04

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 -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.3).

BP6

Variant 11-119019312-C-T is Benign according to our data. Variant chr11-119019312-C-T is described in ClinVar as [Benign]. Clinvar id is 1275542.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.345C>T	p.Phe115Phe	synonymous_variant	2/5	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.345C>T	p.Phe115Phe	synonymous_variant	2/5	1	NM_016146.6	ENSP00000436005.1		Q9Y296-1

Frequencies

GnomAD3 genomes

AF:

0.0848

AC:

12893

AN:

152078

Hom.:

667

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0696

Gnomad AMI

AF:

0.0978

Gnomad AMR

AF:

0.0586

Gnomad ASJ

AF:

0.0325

Gnomad EAS

AF:

0.0779

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.144

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0838

Gnomad OTH

AF:

0.0653

GnomAD3 exomes

AF:

0.0999

AC:

25052

AN:

250734

Hom.:

1696

AF XY:

0.108

AC XY:

14578

AN XY:

135478

show subpopulations

Gnomad AFR exome

AF:

0.0719

Gnomad AMR exome

AF:

0.0625

Gnomad ASJ exome

AF:

0.0402

Gnomad EAS exome

AF:

0.0792

Gnomad SAS exome

AF:

0.220

Gnomad FIN exome

AF:

0.142

Gnomad NFE exome

AF:

0.0846

Gnomad OTH exome

AF:

0.0781

GnomAD4 exome

AF:

0.0959

AC:

140023

AN:

1460114

Hom.:

7871

Cov.:

AF XY:

0.0995

AC XY:

72223

AN XY:

726028

show subpopulations

Gnomad4 AFR exome

AF:

0.0668

Gnomad4 AMR exome

AF:

0.0622

Gnomad4 ASJ exome

AF:

0.0399

Gnomad4 EAS exome

AF:

0.0959

Gnomad4 SAS exome

AF:

0.220

Gnomad4 FIN exome

AF:

0.137

Gnomad4 NFE exome

AF:

0.0881

Gnomad4 OTH exome

AF:

0.0915

GnomAD4 genome

AF:

0.0848

AC:

12905

AN:

152196

Hom.:

669

Cov.:

AF XY:

0.0889

AC XY:

6616

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.0696

Gnomad4 AMR

AF:

0.0585

Gnomad4 ASJ

AF:

0.0325

Gnomad4 EAS

AF:

0.0781

Gnomad4 SAS

AF:

0.233

Gnomad4 FIN

AF:

0.144

Gnomad4 NFE

AF:

0.0838

Gnomad4 OTH

AF:

0.0693

Alfa

AF:

0.0792

Hom.:

478

Bravo

AF:

0.0740

Asia WGS

AF:

0.161

AC:

561

AN:

3478

EpiCase

AF:

0.0823

EpiControl

AF:

0.0852

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 05, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.30

CADD

Benign

DANN

Benign

0.95

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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.

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