Variant 14-39154329-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001079537.2(TRAPPC6B):c.268-35A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 1,308,236 control chromosomes in the GnomAD database, including 43,509 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.20 ( 3830 hom., cov: 32)

Exomes 𝑓: 0.26 ( 39679 hom. )

Consequence

TRAPPC6B
NM_001079537.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.395

Variant links:

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]

TRAPPC6B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 14-39154329-T-C is Benign according to our data. Variant chr14-39154329-T-C is described in ClinVar as [Benign]. Clinvar id is 1342266.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRAPPC6B	NM_001079537.2 linkuse as main transcript	c.268-35A>G		intron_variant		ENST00000330149.10
TRAPPC6B	NM_177452.4 linkuse as main transcript	c.268-2490A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAPPC6B	ENST00000330149.10 linkuse as main transcript	c.268-35A>G		intron_variant		1	NM_001079537.2	P1	Q86SZ2-1

Frequencies

GnomAD3 genomes

AF:

0.199

AC:

30220

AN:

151982

Hom.:

3836

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0484

Gnomad AMI

AF:

0.282

Gnomad AMR

AF:

0.216

Gnomad ASJ

AF:

0.413

Gnomad EAS

AF:

0.224

Gnomad SAS

AF:

0.283

Gnomad FIN

AF:

0.244

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.257

Gnomad OTH

AF:

0.257

GnomAD3 exomes

AF:

0.248

AC:

58223

AN:

234610

Hom.:

7929

AF XY:

0.258

AC XY:

33002

AN XY:

127756

show subpopulations

Gnomad AFR exome

AF:

0.0413

Gnomad AMR exome

AF:

0.193

Gnomad ASJ exome

AF:

0.424

Gnomad EAS exome

AF:

0.241

Gnomad SAS exome

AF:

0.289

Gnomad FIN exome

AF:

0.248

Gnomad NFE exome

AF:

0.265

Gnomad OTH exome

AF:

0.280

GnomAD4 exome

AF:

0.262

AC:

302899

AN:

1156136

Hom.:

39679

Cov.:

AF XY:

0.265

AC XY:

156225

AN XY:

589040

show subpopulations

Gnomad4 AFR exome

AF:

0.0449

Gnomad4 AMR exome

AF:

0.194

Gnomad4 ASJ exome

AF:

0.424

Gnomad4 EAS exome

AF:

0.229

Gnomad4 SAS exome

AF:

0.295

Gnomad4 FIN exome

AF:

0.252

Gnomad4 NFE exome

AF:

0.266

Gnomad4 OTH exome

AF:

0.266

GnomAD4 genome

AF:

0.199

AC:

30206

AN:

152100

Hom.:

3830

Cov.:

AF XY:

0.200

AC XY:

14866

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.0483

Gnomad4 AMR

AF:

0.215

Gnomad4 ASJ

AF:

0.413

Gnomad4 EAS

AF:

0.224

Gnomad4 SAS

AF:

0.283

Gnomad4 FIN

AF:

0.244

Gnomad4 NFE

AF:

0.257

Gnomad4 OTH

AF:

0.254

Alfa

AF:

0.246

Hom.:

1245

Bravo

AF:

0.188

Asia WGS

AF:

0.195

AC:

678

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Neurodevelopmental disorder with microcephaly, epilepsy, and brain atrophy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

6.2

DANN

Benign

0.83

La Branchor

0.63

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over