rs12549048

chr8-140300545-G-Achr8-140300545-G-T

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_001160372.4(TRAPPC9):c.1692C>T(p.Asn564=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 1,613,968 control chromosomes in the GnomAD database, including 44,741 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.24 (4965 hom., cov: 33)
  • Exomes 𝑓: 0.21 (39776 hom.)
• Consequence: TRAPPC9 NM_001160372.4 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:7
• Conservation: PhyloP100: 0.239

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 -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BP6: Variant 8-140300545-G-A is Benign according to our data. Variant chr8-140300545-G-A is described in ClinVar as [Benign]. Clinvar id is 130622.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-140300545-G-A is described in Lovd as [Benign].
• BP7: Synonymous conserved (PhyloP=0.239 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRAPPC9	NM_001160372.4	c.1692C>T	p.Asn564=	synonymous_variant	11/23	ENST00000438773.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAPPC9	ENST00000438773.4	c.1692C>T	p.Asn564=	synonymous_variant	11/23	1	NM_001160372.4	P1
TRAPPC9	ENST00000520857.5	c.1224C>T	p.Asn408=	synonymous_variant	9/21	1
TRAPPC9	ENST00000648948.2	c.1692C>T	p.Asn564=	synonymous_variant	11/23			P1
TRAPPC9	ENST00000521167.1	n.221C>T		non_coding_transcript_exon_variant	2/5	4

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35846 AN: 152036 Hom.: 4957 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.213

GnomAD3 exomes AF: 0.276 AC: 69455 AN: 251486 Hom.: 12086 AF XY: 0.272 AC XY: 36919 AN XY: 135920

Gnomad AFR exome AF: 0.235

Gnomad AMR exome AF: 0.404

Gnomad ASJ exome AF: 0.178

Gnomad EAS exome AF: 0.638

Gnomad SAS exome AF: 0.361

Gnomad FIN exome AF: 0.265

Gnomad NFE exome AF: 0.175

Gnomad OTH exome AF: 0.231

GnomAD4 exome AF: 0.214 AC: 312320 AN: 1461814 Hom.: 39776 Cov.: 35 AF XY: 0.217 AC XY: 157648 AN XY: 727212

Gnomad4 AFR exome AF: 0.229

Gnomad4 AMR exome AF: 0.397

Gnomad4 ASJ exome AF: 0.175

Gnomad4 EAS exome AF: 0.599

Gnomad4 SAS exome AF: 0.360

Gnomad4 FIN exome AF: 0.253

Gnomad4 NFE exome AF: 0.179

Gnomad4 OTH exome AF: 0.231

GnomAD4 genome AF: 0.236 AC: 35870 AN: 152154 Hom.: 4965 Cov.: 33 AF XY: 0.245 AC XY: 18230 AN XY: 74380

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.212

Alfa AF: 0.193 Hom.: 1552

Bravo AF: 0.238

Asia WGS AF: 0.446 AC: 1554 AN: 3478

EpiCase AF: 0.171

EpiControl AF: 0.167

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:2

Likely benign, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	-	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -

Inborn genetic diseases Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 13, 2016

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Intellectual disability, autosomal recessive 13 Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

Intellectual Disability, Recessive Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
Cadd	Benign	5.0
Dann	Benign	0.70

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: rs12549048; hg19: chr8-141310644; COSMIC: COSV66900380;