8-139812378-C-T

Position:

• chr8-139812378-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001160372.4(TRAPPC9):​c.3055+73501G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,964 control chromosomes in the GnomAD database, including 18,226 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (18226 hom., cov: 33)
• Consequence: TRAPPC9 NM_001160372.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

TRAPPC9 (HGNC:30832): (trafficking protein particle complex subunit 9) This gene encodes a protein that likely plays a role in NF-kappa-B signaling. Mutations in this gene have been associated with autosomal-recessive cognitive disability. Alternatively spliced transcript variants have been described.[provided by RefSeq, Feb 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRAPPC9	NM_001160372.4	c.3055+73501G>A		intron_variant		ENST00000438773.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAPPC9	ENST00000438773.4	c.3055+73501G>A		intron_variant		1	NM_001160372.4	P1

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73602 AN: 151846 Hom.: 18207 Cov.: 33

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.491

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.485 AC: 73667 AN: 151964 Hom.: 18226 Cov.: 33 AF XY: 0.485 AC XY: 36041 AN XY: 74260

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.489

Alfa AF: 0.505 Hom.: 2770

Bravo AF: 0.469

Asia WGS AF: 0.378 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.66

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: rs11166930; hg19: chr8-140824621;