8-139951684-T-C

Position:

• chr8-139951684-T-C

Variant summary

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

The NM_001160372.4(TRAPPC9):​c.2810+37042A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.892 in 152,268 control chromosomes in the GnomAD database, including 60,778 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 0.89 (60778 hom., cov: 33)
• Consequence: TRAPPC9 NM_001160372.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254

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]

TRAPPC9 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRAPPC9	NM_001160372.4	c.2810+37042A>G		intron_variant		ENST00000438773.4	NP_001153844.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRAPPC9	ENST00000438773.4	c.2810+37042A>G		intron_variant		1	NM_001160372.4	ENSP00000405060.3

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135779 AN: 152150 Hom.: 60735 Cov.: 33

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.979

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.892 AC: 135878 AN: 152268 Hom.: 60778 Cov.: 33 AF XY: 0.892 AC XY: 66403 AN XY: 74434

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.941

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.894

Gnomad4 FIN AF: 0.888

Gnomad4 NFE AF: 0.891

Gnomad4 OTH AF: 0.907

Alfa AF: 0.874 Hom.: 10479

Bravo AF: 0.883

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs881378; hg19: chr8-140963979;