Variant 2-85326661-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000377386.8(TGOLN2):c.1071G>A(p.Gly357=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 1,613,792 control chromosomes in the GnomAD database, including 255,151 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.57 ( 25447 hom., cov: 32)

Exomes 𝑓: 0.56 ( 229704 hom. )

Consequence

TGOLN2
ENST00000377386.8 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07

Variant links:

Genes affected

TGOLN2 (HGNC:15450): (trans-golgi network protein 2) This gene encodes a type I integral membrane protein that is localized to the trans-Golgi network, a major sorting station for secretory and membrane proteins. The encoded protein cycles between early endosomes and the trans-Golgi network, and may play a role in exocytic vesicle formation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011]

TGOLN2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP7

Synonymous conserved (PhyloP=-1.07 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
TGOLN2	NM_006464.4 linkuse as main transcript	c.1071G>A	p.Gly357=	synonymous_variant	2/4	ENST00000377386.8	NP_006455.2
TGOLN2	NM_001368095.1 linkuse as main transcript	c.1071G>A	p.Gly357=	synonymous_variant	2/4		NP_001355024.1
TGOLN2	NM_001368096.1 linkuse as main transcript	c.1071G>A	p.Gly357=	synonymous_variant	2/4		NP_001355025.1
TGOLN2	NM_001206844.2 linkuse as main transcript	c.897G>A	p.Gly299=	synonymous_variant	3/5		NP_001193773.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TGOLN2	ENST00000377386.8 linkuse as main transcript	c.1071G>A	p.Gly357=	synonymous_variant	2/4	1	NM_006464.4	ENSP00000366603	A2	O43493-2

Frequencies

GnomAD3 genomes

AF:

0.573

AC:

87001

AN:

151966

Hom.:

25430

Cov.:

show subpopulations

Gnomad AFR

AF:

0.545

Gnomad AMI

AF:

0.535

Gnomad AMR

AF:

0.671

Gnomad ASJ

AF:

0.661

Gnomad EAS

AF:

0.882

Gnomad SAS

AF:

0.643

Gnomad FIN

AF:

0.591

Gnomad MID

AF:

0.739

Gnomad NFE

AF:

0.529

Gnomad OTH

AF:

0.608

GnomAD3 exomes

AF:

0.613

AC:

152682

AN:

249266

Hom.:

48453

AF XY:

0.609

AC XY:

82377

AN XY:

135230

show subpopulations

Gnomad AFR exome

AF:

0.553

Gnomad AMR exome

AF:

0.741

Gnomad ASJ exome

AF:

0.649

Gnomad EAS exome

AF:

0.887

Gnomad SAS exome

AF:

0.645

Gnomad FIN exome

AF:

0.592

Gnomad NFE exome

AF:

0.529

Gnomad OTH exome

AF:

0.618

GnomAD4 exome

AF:

0.555

AC:

811260

AN:

1461708

Hom.:

229704

Cov.:

AF XY:

0.558

AC XY:

405420

AN XY:

727138

show subpopulations

Gnomad4 AFR exome

AF:

0.554

Gnomad4 AMR exome

AF:

0.734

Gnomad4 ASJ exome

AF:

0.647

Gnomad4 EAS exome

AF:

0.875

Gnomad4 SAS exome

AF:

0.643

Gnomad4 FIN exome

AF:

0.593

Gnomad4 NFE exome

AF:

0.523

Gnomad4 OTH exome

AF:

0.586

GnomAD4 genome

AF:

0.572

AC:

87054

AN:

152084

Hom.:

25447

Cov.:

AF XY:

0.580

AC XY:

43106

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.545

Gnomad4 AMR

AF:

0.672

Gnomad4 ASJ

AF:

0.661

Gnomad4 EAS

AF:

0.882

Gnomad4 SAS

AF:

0.642

Gnomad4 FIN

AF:

0.591

Gnomad4 NFE

AF:

0.529

Gnomad4 OTH

AF:

0.612

Alfa

AF:

0.548

Hom.:

33105

Bravo

AF:

0.581

Asia WGS

AF:

0.768

AC:

2669

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

4.6

DANN

Benign

0.87

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.0

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over