14-39151847-G-GA

Position:

• chr14-39151847-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.352-9_352-8insT 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 0.00565 in 1,558,592 control chromosomes in the GnomAD database, including 376 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.030 (237 hom., cov: 33)
  • Exomes 𝑓: 0.0030 (139 hom.)
• Consequence: TRAPPC6B NM_001079537.2 splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.01

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 14-39151847-G-GA is Benign according to our data. Variant chr14-39151847-G-GA is described in ClinVar as [Benign]. Clinvar id is 771901.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.352-9_352-8insT		splice_polypyrimidine_tract_variant, intron_variant		ENST00000330149.10
TRAPPC6B	NM_177452.4	c.268-9_268-8insT		splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAPPC6B	ENST00000330149.10	c.352-9_352-8insT		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001079537.2	P1

Frequencies

GnomAD3 genomes AF: 0.0302 AC: 4551 AN: 150942 Hom.: 237 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0101

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000209

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.000561

Gnomad OTH AF: 0.0231

GnomAD3 exomes AF: 0.00879 AC: 1895 AN: 215626 Hom.: 94 AF XY: 0.00664 AC XY: 780 AN XY: 117476

Gnomad AFR exome AF: 0.106

Gnomad AMR exome AF: 0.00575

Gnomad ASJ exome AF: 0.0131

Gnomad EAS exome AF: 0.0000642

Gnomad SAS exome AF: 0.0000418

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000477

Gnomad OTH exome AF: 0.00596

GnomAD4 exome AF: 0.00302 AC: 4250 AN: 1407532 Hom.: 139 Cov.: 25 AF XY: 0.00270 AC XY: 1895 AN XY: 701224

Gnomad4 AFR exome AF: 0.0984

Gnomad4 AMR exome AF: 0.00581

Gnomad4 ASJ exome AF: 0.0112

Gnomad4 EAS exome AF: 0.0000518

Gnomad4 SAS exome AF: 0.0000889

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000319

Gnomad4 OTH exome AF: 0.00661

GnomAD4 genome AF: 0.0302 AC: 4558 AN: 151060 Hom.: 237 Cov.: 33 AF XY: 0.0307 AC XY: 2267 AN XY: 73784

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0101

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000561

Gnomad4 OTH AF: 0.0229

Bravo AF: 0.0335

Asia WGS AF: 0.00346 AC: 12 AN: 3478

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

Invitae

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: rs144205574; hg19: chr14-39621051;