Variant 4-183663862-G-A 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_021942.6(TRAPPC11):c.-6G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0366 in 1,600,768 control chromosomes in the GnomAD database, including 1,425 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.056 ( 300 hom., cov: 31)

Exomes 𝑓: 0.035 ( 1125 hom. )

Consequence

TRAPPC11
NM_021942.6 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0560

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 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=-0.82).

BP6

Variant 4-183663862-G-A is Benign according to our data. Variant chr4-183663862-G-A is described in ClinVar as [Benign]. Clinvar id is 261440.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-183663862-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRAPPC11	NM_021942.6 linkuse as main transcript	c.-6G>A		5_prime_UTR_variant	2/30	ENST00000334690.11

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAPPC11	ENST00000334690.11 linkuse as main transcript	c.-6G>A	5_prime_UTR_variant	2/30	1	NM_021942.6	P1	Q7Z392-1
TRAPPC11	ENST00000357207.8 linkuse as main transcript	c.-6G>A	5_prime_UTR_variant	2/31	1			Q7Z392-3
TRAPPC11	ENST00000505676.5 linkuse as main transcript	c.-6G>A	5_prime_UTR_variant, NMD_transcript_variant	2/19	1
TRAPPC11	ENST00000504526.1 linkuse as main transcript	n.141G>A	non_coding_transcript_exon_variant	2/3	4

Frequencies

GnomAD3 genomes

AF:

0.0556

AC:

8386

AN:

150932

Hom.:

297

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0988

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.0446

Gnomad ASJ

AF:

0.0312

Gnomad EAS

AF:

0.000196

Gnomad SAS

AF:

0.00670

Gnomad FIN

AF:

0.0887

Gnomad MID

AF:

0.0541

Gnomad NFE

AF:

0.0365

Gnomad OTH

AF:

0.0491

GnomAD3 exomes

AF:

0.0365

AC:

9137

AN:

250512

Hom.:

280

AF XY:

0.0344

AC XY:

4655

AN XY:

135432

show subpopulations

Gnomad AFR exome

AF:

0.100

Gnomad AMR exome

AF:

0.0271

Gnomad ASJ exome

AF:

0.0313

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.00734

Gnomad FIN exome

AF:

0.0792

Gnomad NFE exome

AF:

0.0361

Gnomad OTH exome

AF:

0.0379

GnomAD4 exome

AF:

0.0346

AC:

50203

AN:

1449720

Hom.:

1125

Cov.:

AF XY:

0.0337

AC XY:

24302

AN XY:

721132

show subpopulations

Gnomad4 AFR exome

AF:

0.103

Gnomad4 AMR exome

AF:

0.0282

Gnomad4 ASJ exome

AF:

0.0307

Gnomad4 EAS exome

AF:

0.000128

Gnomad4 SAS exome

AF:

0.00743

Gnomad4 FIN exome

AF:

0.0804

Gnomad4 NFE exome

AF:

0.0340

Gnomad4 OTH exome

AF:

0.0367

GnomAD4 genome

AF:

0.0557

AC:

8416

AN:

151048

Hom.:

300

Cov.:

AF XY:

0.0578

AC XY:

4262

AN XY:

73728

show subpopulations

Gnomad4 AFR

AF:

0.0992

Gnomad4 AMR

AF:

0.0445

Gnomad4 ASJ

AF:

0.0312

Gnomad4 EAS

AF:

0.000197

Gnomad4 SAS

AF:

0.00671

Gnomad4 FIN

AF:

0.0887

Gnomad4 NFE

AF:

0.0365

Gnomad4 OTH

AF:

0.0491

Alfa

AF:

0.0417

Hom.:

103

Bravo

AF:

0.0529

Asia WGS

AF:

0.0230

AC:

AN:

3478

EpiCase

AF:

0.0363

EpiControl

AF:

0.0353

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

Cadd

Benign

4.6

Dann

Benign

0.81

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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