chr4-183663736-GT-G

Variant names:

• chr4-183663736-GT-G
• rs70959134
• NM_021942.6:c.-21-92delT

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BS1

The NM_021942.6(TRAPPC11):​c.-21-92delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0171 in 386,590 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 0.0039 (0 hom., cov: 0)
  • Exomes 𝑓: 0.022 (0 hom.)
• Consequence: TRAPPC11 NM_021942.6 intron
• Clinical Significance: Not reported in ClinVar
• 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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00387 (418/108042) while in subpopulation SAS AF= 0.00867 (28/3228). AF 95% confidence interval is 0.0068. There are 0 homozygotes in gnomad4. There are 202 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAPPC11	NM_021942.6	c.-21-92delT		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.-21-110delT		intron_variant	Intron 1 of 29	1	NM_021942.6	ENSP00000335371.6
TRAPPC11	ENST00000357207.8	c.-21-110delT		intron_variant	Intron 1 of 30	1		ENSP00000349738.4
TRAPPC11	ENST00000505676.5	n.-21-110delT		intron_variant	Intron 1 of 18	1		ENSP00000422915.1
TRAPPC11	ENST00000504526.1	n.126-110delT		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.00386 AC: 417 AN: 108050 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00759

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00387

Gnomad ASJ AF: 0.000706

Gnomad EAS AF: 0.00610

Gnomad SAS AF: 0.00866

Gnomad FIN AF: 0.00150

Gnomad MID AF: 0.00463

Gnomad NFE AF: 0.00166

Gnomad OTH AF: 0.00546

GnomAD4 exome AF: 0.0222 AC: 6193 AN: 278548 Hom.: 0 AF XY: 0.0229 AC XY: 3356 AN XY: 146246

Gnomad4 AFR exome AF: 0.0256

Gnomad4 AMR exome AF: 0.0364

Gnomad4 ASJ exome AF: 0.0127

Gnomad4 EAS exome AF: 0.0185

Gnomad4 SAS exome AF: 0.0438

Gnomad4 FIN exome AF: 0.0144

Gnomad4 NFE exome AF: 0.0199

Gnomad4 OTH exome AF: 0.0191

GnomAD4 genome AF: 0.00387 AC: 418 AN: 108042 Hom.: 0 Cov.: 0 AF XY: 0.00396 AC XY: 202 AN XY: 51064

Gnomad4 AFR AF: 0.00762

Gnomad4 AMR AF: 0.00387

Gnomad4 ASJ AF: 0.000706

Gnomad4 EAS AF: 0.00613

Gnomad4 SAS AF: 0.00867

Gnomad4 FIN AF: 0.00150

Gnomad4 NFE AF: 0.00166

Gnomad4 OTH AF: 0.00544

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;