chr14-39150383-T-TA

Position:

• chr14-39150383-T-TA

Variant summary

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

The NM_001079537.2(TRAPPC6B):​c.446-3_446-2insT 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 0.0217 in 1,193,754 control chromosomes in the GnomAD database, including 5 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0013 (3 hom., cov: 31)
  • Exomes 𝑓: 0.025 (2 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-T-TA is Benign according to our data. Variant chr14-39150383-T-TA is described in ClinVar as [Benign]. Clinvar id is 1987185.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRAPPC6B	NM_001079537.2	c.446-3_446-2insT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000330149.10
TRAPPC6B	NM_177452.4	c.362-3_362-2insT		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.446-3_446-2insT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_001079537.2	P1
	ENST00000648024.1	n.2562dup		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.00126 AC: 184 AN: 146602 Hom.: 3 Cov.: 31

Gnomad AFR AF: 0.000225

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000685

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0282

Gnomad SAS AF: 0.00171

Gnomad FIN AF: 0.000108

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000181

Gnomad OTH AF: 0.000505

GnomAD4 exome AF: 0.0246 AC: 25717 AN: 1047090 Hom.: 2 Cov.: 19 AF XY: 0.0239 AC XY: 12380 AN XY: 517888

Gnomad4 AFR exome AF: 0.0288

Gnomad4 AMR exome AF: 0.0283

Gnomad4 ASJ exome AF: 0.0268

Gnomad4 EAS exome AF: 0.0574

Gnomad4 SAS exome AF: 0.0250

Gnomad4 FIN exome AF: 0.0172

Gnomad4 NFE exome AF: 0.0235

Gnomad4 OTH exome AF: 0.0246

GnomAD4 genome AF: 0.00125 AC: 184 AN: 146664 Hom.: 3 Cov.: 31 AF XY: 0.00153 AC XY: 109 AN XY: 71302

Gnomad4 AFR AF: 0.000224

Gnomad4 AMR AF: 0.000685

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0283

Gnomad4 SAS AF: 0.00171

Gnomad4 FIN AF: 0.000108

Gnomad4 NFE AF: 0.000181

Gnomad4 OTH AF: 0.000500

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

Jul 24, 2022

- -

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: rs150886646; hg19: chr14-39619587;