rs1870805

chr8-139985033-G-Achr8-139985033-G-T

Variant summary

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

The NM_001160372.4(TRAPPC9):c.2810+3693C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,002 control chromosomes in the GnomAD database, including 13,833 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 0.42 (13833 hom., cov: 33)
• Consequence: TRAPPC9 NM_001160372.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.843

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRAPPC9	NM_001160372.4	c.2810+3693C>T		intron_variant		ENST00000438773.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAPPC9	ENST00000438773.4	c.2810+3693C>T		intron_variant		1	NM_001160372.4	P1

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64406 AN: 151884 Hom.: 13822 Cov.: 33

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.424 AC: 64451 AN: 152002 Hom.: 13833 Cov.: 33 AF XY: 0.422 AC XY: 31356 AN XY: 74320

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.418

Alfa AF: 0.426 Hom.: 19758

Bravo AF: 0.417

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.4

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1870805; hg19: chr8-140995243;