Variant chr14-39151732-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001079537.2(TRAPPC6B):c.445+14G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.927 in 1,541,016 control chromosomes in the GnomAD database, including 662,790 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.93 ( 65299 hom., cov: 30)

Exomes 𝑓: 0.93 ( 597491 hom. )

Consequence

TRAPPC6B
NM_001079537.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0640

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 14-39151732-C-T is Benign according to our data. Variant chr14-39151732-C-T is described in ClinVar as [Benign]. Clinvar id is 1342265.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 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.445+14G>A		intron_variant		ENST00000330149.10
TRAPPC6B	NM_177452.4 linkuse as main transcript	c.361+14G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRAPPC6B	ENST00000330149.10 linkuse as main transcript	c.445+14G>A		intron_variant		1	NM_001079537.2	P1	Q86SZ2-1

Frequencies

GnomAD3 genomes

AF:

0.927

AC:

140672

AN:

151816

Hom.:

65265

Cov.:

show subpopulations

Gnomad AFR

AF:

0.934

Gnomad AMI

AF:

0.968

Gnomad AMR

AF:

0.874

Gnomad ASJ

AF:

0.920

Gnomad EAS

AF:

0.951

Gnomad SAS

AF:

0.848

Gnomad FIN

AF:

0.931

Gnomad MID

AF:

0.886

Gnomad NFE

AF:

0.937

Gnomad OTH

AF:

0.921

GnomAD3 exomes

AF:

0.918

AC:

186771

AN:

203528

Hom.:

85867

AF XY:

0.916

AC XY:

102275

AN XY:

111598

show subpopulations

Gnomad AFR exome

AF:

0.938

Gnomad AMR exome

AF:

0.850

Gnomad ASJ exome

AF:

0.921

Gnomad EAS exome

AF:

0.954

Gnomad SAS exome

AF:

0.841

Gnomad FIN exome

AF:

0.927

Gnomad NFE exome

AF:

0.939

Gnomad OTH exome

AF:

0.918

GnomAD4 exome

AF:

0.927

AC:

1287743

AN:

1389084

Hom.:

597491

Cov.:

AF XY:

0.926

AC XY:

640258

AN XY:

691704

show subpopulations

Gnomad4 AFR exome

AF:

0.931

Gnomad4 AMR exome

AF:

0.852

Gnomad4 ASJ exome

AF:

0.918

Gnomad4 EAS exome

AF:

0.968

Gnomad4 SAS exome

AF:

0.841

Gnomad4 FIN exome

AF:

0.924

Gnomad4 NFE exome

AF:

0.934

Gnomad4 OTH exome

AF:

0.921

GnomAD4 genome

AF:

0.926

AC:

140761

AN:

151932

Hom.:

65299

Cov.:

AF XY:

0.923

AC XY:

68536

AN XY:

74266

show subpopulations

Gnomad4 AFR

AF:

0.934

Gnomad4 AMR

AF:

0.873

Gnomad4 ASJ

AF:

0.920

Gnomad4 EAS

AF:

0.952

Gnomad4 SAS

AF:

0.848

Gnomad4 FIN

AF:

0.931

Gnomad4 NFE

AF:

0.937

Gnomad4 OTH

AF:

0.916

Alfa

AF:

0.927

Hom.:

10929

Bravo

AF:

0.924

Asia WGS

AF:

0.877

AC:

3039

AN:

3462

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

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

-0.84

CADD

Benign

5.9

DANN

Benign

0.51

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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