14-39150383-TA-T

Position:

• chr14-39150383-TA-T

Variant summary

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

The NM_001079537.2(TRAPPC6B):​c.446-3del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 1,141,986 control chromosomes in the GnomAD database, including 2,040 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.043 (170 hom., cov: 31)
  • Exomes 𝑓: 0.12 (1870 hom.)
• Consequence: TRAPPC6B NM_001079537.2 splice_region, splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0690

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 14-39150383-TA-T is Benign according to our data. Variant chr14-39150383-TA-T is described in ClinVar as [Benign]. Clinvar id is 1598887.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRAPPC6B	NM_001079537.2	c.446-3del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000330149.10
TRAPPC6B	NM_177452.4	c.362-3del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAPPC6B	ENST00000330149.10	c.446-3del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_001079537.2	P1
	ENST00000648024.1	n.2562del		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.0435 AC: 6368 AN: 146486 Hom.: 170 Cov.: 31

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0179

Gnomad AMR AF: 0.0367

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.00336

Gnomad SAS AF: 0.0252

Gnomad FIN AF: 0.0465

Gnomad MID AF: 0.00987

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.0374

GnomAD4 exome AF: 0.115 AC: 114568 AN: 995442 Hom.: 1870 Cov.: 19 AF XY: 0.115 AC XY: 56277 AN XY: 490536

Gnomad4 AFR exome AF: 0.0540

Gnomad4 AMR exome AF: 0.0876

Gnomad4 ASJ exome AF: 0.0653

Gnomad4 EAS exome AF: 0.0432

Gnomad4 SAS exome AF: 0.0865

Gnomad4 FIN exome AF: 0.102

Gnomad4 NFE exome AF: 0.124

Gnomad4 OTH exome AF: 0.111

GnomAD4 genome AF: 0.0434 AC: 6365 AN: 146544 Hom.: 170 Cov.: 31 AF XY: 0.0404 AC XY: 2876 AN XY: 71232

Gnomad4 AFR AF: 0.0123

Gnomad4 AMR AF: 0.0366

Gnomad4 ASJ AF: 0.0109

Gnomad4 EAS AF: 0.00336

Gnomad4 SAS AF: 0.0253

Gnomad4 FIN AF: 0.0465

Gnomad4 NFE AF: 0.0700

Gnomad4 OTH AF: 0.0365

Bravo AF: 0.0399

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

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs150886646; hg19: chr14-39619587;