Genetic Variant TRAPPC3:c.424-20G>A (chr1-36137342-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_014408.5(TRAPPC3):c.424-20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 1,599,800 control chromosomes in the GnomAD database, including 458,586 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.77 ( 45654 hom., cov: 31)

Exomes 𝑓: 0.75 ( 412932 hom. )

Consequence

TRAPPC3
NM_014408.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.00700

Variant links:

Genes affected

TRAPPC3 (HGNC:19942): (trafficking protein particle complex subunit 3) This gene encodes a component of the trafficking protein particle complex, which tethers transport vesicles to the cis-Golgi membrane. The encoded protein participates in the regulation of transport from the endoplasmic reticulum to the Golgi apparatus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

TRAPPC3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

This position, referring to a specific DNA site, is a probable branch point but is likely benign (scored 2 / 10, using the threshold of <=3). The score ranges from 0 to 10, with values ≤3 considered benign and >5 classified as pathogenic. Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 1-36137342-C-T is Benign according to our data. Variant chr1-36137342-C-T is described in ClinVar as [Benign]. Clinvar id is 1601300.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAPPC3	NM_014408.5 link	c.424-20G>A		intron_variant	Intron 4 of 4	ENST00000373166.8	NP_055223.1	O43617-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRAPPC3	ENST00000373166.8 link	c.424-20G>A		intron_variant	Intron 4 of 4	1	NM_014408.5	ENSP00000362261.3		O43617-1

Frequencies

GnomAD3 genomes

AF:

0.772

AC:

117242

AN:

151952

Hom.:

45596

Cov.:

show subpopulations

Gnomad AFR

AF:

0.834

Gnomad AMI

AF:

0.657

Gnomad AMR

AF:

0.820

Gnomad ASJ

AF:

0.657

Gnomad EAS

AF:

0.702

Gnomad SAS

AF:

0.662

Gnomad FIN

AF:

0.665

Gnomad MID

AF:

0.722

Gnomad NFE

AF:

0.760

Gnomad OTH

AF:

0.755

GnomAD3 exomes

AF:

0.745

AC:

185998

AN:

249674

Hom.:

69957

AF XY:

0.738

AC XY:

99673

AN XY:

135048

show subpopulations

Gnomad AFR exome

AF:

0.839

Gnomad AMR exome

AF:

0.844

Gnomad ASJ exome

AF:

0.660

Gnomad EAS exome

AF:

0.713

Gnomad SAS exome

AF:

0.659

Gnomad FIN exome

AF:

0.666

Gnomad NFE exome

AF:

0.752

Gnomad OTH exome

AF:

0.742

GnomAD4 exome

AF:

0.754

AC:

1091423

AN:

1447730

Hom.:

412932

Cov.:

AF XY:

0.750

AC XY:

538161

AN XY:

717244

show subpopulations

Gnomad4 AFR exome

AF:

0.836

Gnomad4 AMR exome

AF:

0.838

Gnomad4 ASJ exome

AF:

0.659

Gnomad4 EAS exome

AF:

0.724

Gnomad4 SAS exome

AF:

0.663

Gnomad4 FIN exome

AF:

0.672

Gnomad4 NFE exome

AF:

0.763

Gnomad4 OTH exome

AF:

0.745

GnomAD4 genome

AF:

0.772

AC:

117367

AN:

152070

Hom.:

45654

Cov.:

AF XY:

0.766

AC XY:

56908

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.834

Gnomad4 AMR

AF:

0.820

Gnomad4 ASJ

AF:

0.657

Gnomad4 EAS

AF:

0.703

Gnomad4 SAS

AF:

0.663

Gnomad4 FIN

AF:

0.665

Gnomad4 NFE

AF:

0.760

Gnomad4 OTH

AF:

0.756

Alfa

AF:

0.752

Hom.:

7840

Bravo

AF:

0.788

Asia WGS

AF:

0.696

AC:

2423

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

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.8

DANN

Benign

0.58

BranchPoint Hunter

2.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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