chrX-13713103-CA-C

Variant names:

• chrX-13713103-CA-C
• rs35590746
• NM_001011658.4:c.*1303delT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001011658.4(TRAPPC2):​c.*1303delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.31 (2617 hom., 2731 hem., cov: 5)
  • Exomes 𝑓: 0.071 (0 hom. 0 hem.)
• Consequence: TRAPPC2 NM_001011658.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.108

Genes affected

TRAPPC2 (HGNC:23068): (trafficking protein particle complex subunit 2) The protein encoded by this gene is thought to be part of a large multi-subunit complex involved in the targeting and fusion of endoplasmic reticulum-to-Golgi transport vesicles with their acceptor compartment. In addition, the encoded protein can bind c-myc promoter-binding protein 1 and block its transcriptional repression capability. Mutations in this gene are a cause of spondyloepiphyseal dysplasia tarda (SEDT). A processed pseudogene of this gene is located on chromosome 19, and other pseudogenes are found on chromosomes 8 and Y. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant X-13713103-CA-C is Benign according to our data. Variant chrX-13713103-CA-C is described in ClinVar as [Benign]. Clinvar id is 367970.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAPPC2	NM_001011658.4	c.*1303delT		3_prime_UTR_variant	Exon 6 of 6	ENST00000380579.6	NP_001011658.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRAPPC2	ENST00000380579	c.*1303delT		3_prime_UTR_variant	Exon 6 of 6	1	NM_001011658.4	ENSP00000369953.1
TRAPPC2	ENST00000683983	c.*1303delT		3_prime_UTR_variant	Exon 6 of 6			ENSP00000507474.1
TRAPPC2	ENST00000359680	c.*1303delT		3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000352708.5
TRAPPC2	ENST00000683569	c.*1303delT		3_prime_UTR_variant	Exon 7 of 7			ENSP00000508155.1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 21487 AN: 68727 Hom.: 2612 Cov.: 5 AF XY: 0.242 AC XY: 2728 AN XY: 11273

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.378

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.335

GnomAD4 exome AF: 0.0714 AC: 7 AN: 98 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 68

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0875

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.313 AC: 21486 AN: 68704 Hom.: 2617 Cov.: 5 AF XY: 0.242 AC XY: 2731 AN XY: 11274

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.339

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Spondyloepiphyseal dysplasia congenita Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

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: rs35590746; hg19: chrX-13731222;