4-183663736-G-GT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_021942.6(TRAPPC11):c.-21-92dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 388,094 control chromosomes in the GnomAD database, including 5,062 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.29 (4405 hom., cov: 0)
  • Exomes 𝑓: 0.035 (657 hom.)
• Consequence: TRAPPC11 NM_021942.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.751

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 4-183663736-G-GT is Benign according to our data. Variant chr4-183663736-G-GT is described in ClinVar as [Benign]. Clinvar id is 1296244.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRAPPC11	NM_021942.6	c.-21-92dup		intron_variant		ENST00000334690.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAPPC11	ENST00000334690.11	c.-21-92dup		intron_variant		1	NM_021942.6	P1
TRAPPC11	ENST00000357207.8	c.-21-92dup		intron_variant		1
TRAPPC11	ENST00000505676.5	c.-21-92dup		intron_variant, NMD_transcript_variant		1
TRAPPC11	ENST00000504526.1	n.126-92dup		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.294 AC: 31731 AN: 108026 Hom.: 4407 Cov.: 0

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.295

GnomAD4 exome AF: 0.0351 AC: 9821 AN: 280076 Hom.: 657 AF XY: 0.0370 AC XY: 5440 AN XY: 147126

Gnomad4 AFR exome AF: 0.0674

Gnomad4 AMR exome AF: 0.0654

Gnomad4 ASJ exome AF: 0.0264

Gnomad4 EAS exome AF: 0.0270

Gnomad4 SAS exome AF: 0.0648

Gnomad4 FIN exome AF: 0.0186

Gnomad4 NFE exome AF: 0.0309

Gnomad4 OTH exome AF: 0.0281

GnomAD4 genome AF: 0.294 AC: 31733 AN: 108018 Hom.: 4405 Cov.: 0 AF XY: 0.287 AC XY: 14651 AN XY: 51068

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.294

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 14, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs70959134; hg19: chr4-184584889;