4-183663736-GTTTTTTTT-GTTTT

Variant names:

• chr4-183663736-GTTTT-G
• rs70959134
• NM_021942.6:c.-21-95_-21-92delTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_021942.6(TRAPPC11):​c.-21-95_-21-92delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000529 in 387,544 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00022 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00065 (0 hom.)
• Consequence: TRAPPC11 NM_021942.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.972

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAPPC11	NM_021942.6	c.-21-95_-21-92delTTTT		intron_variant	Intron 1 of 29	ENST00000334690.11	NP_068761.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRAPPC11	ENST00000334690.11	c.-21-110_-21-107delTTTT		intron_variant	Intron 1 of 29	1	NM_021942.6	ENSP00000335371.6
TRAPPC11	ENST00000357207.8	c.-21-110_-21-107delTTTT		intron_variant	Intron 1 of 30	1		ENSP00000349738.4
TRAPPC11	ENST00000505676.5	n.-21-110_-21-107delTTTT		intron_variant	Intron 1 of 18	1		ENSP00000422915.1
TRAPPC11	ENST00000504526.1	n.126-110_126-107delTTTT		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.000222 AC: 24 AN: 108058 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000169

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000427

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000331

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000648 AC: 181 AN: 279486 Hom.: 0 AF XY: 0.000545 AC XY: 80 AN XY: 146790

Gnomad4 AFR exome AF: 0.000982

Gnomad4 AMR exome AF: 0.000630

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000504

Gnomad4 SAS exome AF: 0.00108

Gnomad4 FIN exome AF: 0.000295

Gnomad4 NFE exome AF: 0.000649

Gnomad4 OTH exome AF: 0.000757

GnomAD4 genome AF: 0.000222 AC: 24 AN: 108058 Hom.: 0 Cov.: 0 AF XY: 0.000176 AC XY: 9 AN XY: 51064

Gnomad4 AFR AF: 0.000169

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000427

Gnomad4 NFE AF: 0.000331

Gnomad4 OTH AF: 0.00

Bravo AF: 0.000106

ClinVar

Not reported in ClinVar

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;