Variant 7-100157720-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_018275.5(TRAPPC14):c.550G>A(p.Val184Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00471 in 1,614,222 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0031 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0049 ( 31 hom. )

Consequence

TRAPPC14
NM_018275.5 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:2

Conservation

PhyloP100: 3.17

Variant links:

Genes affected

TRAPPC14 (HGNC:25604): (trafficking protein particle complex subunit 14) Enables alpha-tubulin binding activity. Involved in cilium assembly and regulation of cell population proliferation. Located in several cellular components, including microtubule cytoskeleton; midbody; and plasma membrane. Part of TRAPPII protein complex. Implicated in primary autosomal recessive microcephaly. [provided by Alliance of Genome Resources, Apr 2022]

TRAPPC14 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00498724).

BP6

Variant 7-100157720-C-T is Benign according to our data. Variant chr7-100157720-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2657741.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 31 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRAPPC14	NM_018275.5 link	c.550G>A	p.Val184Ile	missense_variant	3/11	ENST00000316937.8	NP_060745.3	Q8WVR3-1
TRAPPC14	NM_001303470.2 link	c.-258G>A		5_prime_UTR_variant	3/11		NP_001290399.1	B3KNS5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRAPPC14	ENST00000316937.8 link	c.550G>A	p.Val184Ile	missense_variant	3/11	1	NM_018275.5	ENSP00000324741.3		Q8WVR3-1

Frequencies

GnomAD3 genomes

AF:

0.00311

AC:

473

AN:

152222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00116

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00268

Gnomad ASJ

AF:

0.00836

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00579

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00472

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00359

AC:

903

AN:

251452

Hom.:

AF XY:

0.00396

AC XY:

538

AN XY:

135902

show subpopulations

Gnomad AFR exome

AF:

0.00135

Gnomad AMR exome

AF:

0.00202

Gnomad ASJ exome

AF:

0.0105

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00673

Gnomad FIN exome

AF:

0.000323

Gnomad NFE exome

AF:

0.00408

Gnomad OTH exome

AF:

0.00456

GnomAD4 exome

AF:

0.00488

AC:

7137

AN:

1461882

Hom.:

Cov.:

AF XY:

0.00508

AC XY:

3694

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.00102

Gnomad4 AMR exome

AF:

0.00201

Gnomad4 ASJ exome

AF:

0.00945

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00729

Gnomad4 FIN exome

AF:

0.000300

Gnomad4 NFE exome

AF:

0.00519

Gnomad4 OTH exome

AF:

0.00556

GnomAD4 genome

AF:

0.00310

AC:

473

AN:

152340

Hom.:

Cov.:

AF XY:

0.00289

AC XY:

215

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.00115

Gnomad4 AMR

AF:

0.00268

Gnomad4 ASJ

AF:

0.00836

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00580

Gnomad4 FIN

AF:

0.0000942

Gnomad4 NFE

AF:

0.00472

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00477

Hom.:

Bravo

AF:

0.00322

TwinsUK

AF:

0.00324

AC:

ALSPAC

AF:

0.00337

AC:

ESP6500AA

AF:

0.000908

AC:

ESP6500EA

AF:

0.00570

AC:

ExAC

AF:

0.00358

AC:

435

Asia WGS

AF:

0.00318

AC:

AN:

3478

EpiCase

AF:

0.00589

EpiControl

AF:

0.00628

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

TRAPPC14-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 25, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

TRAPPC14: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.44

BayesDel_noAF

Benign

-0.41

CADD

Benign

DANN

Benign

0.95

DEOGEN2

Benign

0.024

Eigen

Benign

-0.18

Eigen_PC

Benign

0.066

FATHMM_MKL

Uncertain

0.78

LIST_S2

Benign

0.72

M_CAP

Benign

0.0089

MetaRNN

Benign

0.0050

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.90

PROVEAN

Benign

-0.49

REVEL

Benign

0.13

Sift

Benign

0.73

Sift4G

Benign

0.42

Polyphen

0.15

Vest4

0.20

MVP

0.28

MPC

1.0

ClinPred

0.015

GERP RS

5.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.096

gMVP

0.25

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