4-183663736-G-GTT

Position:

• chr4-183663736-G-GTT

Variant summary

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

The NM_021942.6(TRAPPC11):​c.-21-93_-21-92dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0151 in 388,146 control chromosomes in the GnomAD database, including 284 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.033 (219 hom., cov: 0)
  • Exomes 𝑓: 0.0080 (65 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-GTT is Benign according to our data. Variant chr4-183663736-G-GTT is described in ClinVar as [Benign]. Clinvar id is 1241290.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRAPPC11	NM_021942.6	c.-21-93_-21-92dup		intron_variant		ENST00000334690.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAPPC11	ENST00000334690.11	c.-21-93_-21-92dup		intron_variant		1	NM_021942.6	P1
TRAPPC11	ENST00000357207.8	c.-21-93_-21-92dup		intron_variant		1
TRAPPC11	ENST00000505676.5	c.-21-93_-21-92dup		intron_variant, NMD_transcript_variant		1
TRAPPC11	ENST00000504526.1	n.126-93_126-92dup		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0333 AC: 3601 AN: 108020 Hom.: 219 Cov.: 0

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.00518

Gnomad AMR AF: 0.0136

Gnomad ASJ AF: 0.00177

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.00278

Gnomad FIN AF: 0.000640

Gnomad MID AF: 0.0139

Gnomad NFE AF: 0.00275

Gnomad OTH AF: 0.0219

GnomAD4 exome AF: 0.00800 AC: 2241 AN: 280132 Hom.: 65 AF XY: 0.00810 AC XY: 1192 AN XY: 147166

Gnomad4 AFR exome AF: 0.0264

Gnomad4 AMR exome AF: 0.0152

Gnomad4 ASJ exome AF: 0.00744

Gnomad4 EAS exome AF: 0.00532

Gnomad4 SAS exome AF: 0.0132

Gnomad4 FIN exome AF: 0.00413

Gnomad4 NFE exome AF: 0.00687

Gnomad4 OTH exome AF: 0.00642

GnomAD4 genome AF: 0.0334 AC: 3606 AN: 108014 Hom.: 219 Cov.: 0 AF XY: 0.0318 AC XY: 1625 AN XY: 51054

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0136

Gnomad4 ASJ AF: 0.00177

Gnomad4 EAS AF: 0.00117

Gnomad4 SAS AF: 0.00248

Gnomad4 FIN AF: 0.000640

Gnomad4 NFE AF: 0.00275

Gnomad4 OTH AF: 0.0218

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

Sep 02, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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;