rs4317547

chr8-140274999-A-Cchr8-140274999-A-T

Variant summary

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

The NM_001160372.4(TRAPPC9):c.2278+659T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,072 control chromosomes in the GnomAD database, including 42,493 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 0.74 (42493 hom., cov: 32)
• Consequence: TRAPPC9 NM_001160372.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963

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]

LOC105375779 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRAPPC9	NM_001160372.4	c.2278+659T>G		intron_variant		ENST00000438773.4
LOC105375779	XR_001746117.2	n.69+6041A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAPPC9	ENST00000438773.4	c.2278+659T>G		intron_variant		1	NM_001160372.4	P1

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111872 AN: 151954 Hom.: 42439 Cov.: 32

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.736 AC: 111987 AN: 152072 Hom.: 42493 Cov.: 32 AF XY: 0.725 AC XY: 53890 AN XY: 74336

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.838

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.754

Alfa AF: 0.734 Hom.: 38675

Bravo AF: 0.743

Asia WGS AF: 0.491 AC: 1707 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	1.9
Dann	Benign	0.62

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: rs4317547; hg19: chr8-141285098;