14-39154309-G-GA

Position:

• chr14-39154309-G-GA

Variant summary

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

The NM_001079537.2(TRAPPC6B):​c.268-16_268-15insT variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00569 in 1,569,546 control chromosomes in the GnomAD database, including 381 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.030 (234 hom., cov: 31)
  • Exomes 𝑓: 0.0031 (147 hom.)
• Consequence: TRAPPC6B NM_001079537.2 splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.55

Genes affected

TRAPPC6B (HGNC:23066): (trafficking protein particle complex subunit 6B) TRAPPC6B is a component of TRAPP complexes, which are tethering complexes involved in vesicle transport (Kummel et al., 2005 [PubMed 16025134]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 14-39154309-G-GA is Benign according to our data. Variant chr14-39154309-G-GA is described in ClinVar as [Benign]. Clinvar id is 1544127.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRAPPC6B	NM_001079537.2	c.268-16_268-15insT		splice_polypyrimidine_tract_variant, intron_variant		ENST00000330149.10
TRAPPC6B	NM_177452.4	c.268-2471_268-2470insT		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAPPC6B	ENST00000330149.10	c.268-16_268-15insT		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001079537.2	P1

Frequencies

GnomAD3 genomes AF: 0.0300 AC: 4555 AN: 151724 Hom.: 234 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0100

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000530

Gnomad OTH AF: 0.0231

GnomAD3 exomes AF: 0.00792 AC: 1869 AN: 236034 Hom.: 90 AF XY: 0.00629 AC XY: 808 AN XY: 128554

Gnomad AFR exome AF: 0.105

Gnomad AMR exome AF: 0.00499

Gnomad ASJ exome AF: 0.0146

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000696

Gnomad FIN exome AF: 0.0000475

Gnomad NFE exome AF: 0.000414

Gnomad OTH exome AF: 0.00524

GnomAD4 exome AF: 0.00308 AC: 4369 AN: 1417704 Hom.: 147 Cov.: 23 AF XY: 0.00274 AC XY: 1939 AN XY: 707248

Gnomad4 AFR exome AF: 0.0968

Gnomad4 AMR exome AF: 0.00544

Gnomad4 ASJ exome AF: 0.0117

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000119

Gnomad4 FIN exome AF: 0.0000567

Gnomad4 NFE exome AF: 0.000327

Gnomad4 OTH exome AF: 0.00667

GnomAD4 genome AF: 0.0300 AC: 4562 AN: 151842 Hom.: 234 Cov.: 31 AF XY: 0.0306 AC XY: 2273 AN XY: 74196

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.0100

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000530

Gnomad4 OTH AF: 0.0228

Alfa AF: 0.0183 Hom.: 20

Bravo AF: 0.0335

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 20, 2023

- -

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: rs142476037; hg19: chr14-39623513;