Variant 3-100709442-G-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_001007565.2(TFG):c.-44+11G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0237 in 152,636 control chromosomes in the GnomAD database, including 110 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.024 ( 110 hom., cov: 33)

Exomes 𝑓: 0.0032 ( 0 hom. )

Consequence

TFG
NM_001007565.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -4.80

Variant links:

Genes affected

TFG (HGNC:11758): (trafficking from ER to golgi regulator) There are several documented fusion oncoproteins encoded partially by this gene. This gene also participates in several oncogenic rearrangements resulting in anaplastic lymphoma and mixoid chondrosarcoma, and may play a role in the NF-kappaB pathway. Multiple transcript variants have been found for this gene. [provided by RefSeq, Sep 2010]

TFG links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 3-100709442-G-T is Benign according to our data. Variant chr3-100709442-G-T is described in ClinVar as [Benign]. Clinvar id is 378883.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.069 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TFG	NM_001007565.2 link	c.-44+11G>T		intron_variant	Intron 1 of 7		NP_001007566.1	Q92734-1
TFG	XM_005247066.3 link	c.-44+11G>T		intron_variant	Intron 1 of 7		XP_005247123.1	Q92734-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
TFG	ENST00000675692 link	c.-323G>T	5_prime_UTR_variant	Exon 1 of 9	ENSP00000502034.1	A0A6Q8PFY7
TFG	ENST00000675553 link	c.-190G>T	5_prime_UTR_variant	Exon 1 of 8	ENSP00000501815.1	Q92734-1
TFG	ENST00000674645 link	c.-323G>T	5_prime_UTR_variant	Exon 1 of 8	ENSP00000501892.1	Q92734-2

Frequencies

GnomAD3 genomes

AF:

0.0238

AC:

3617

AN:

152208

Hom.:

109

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0712

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0114

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.00174

Gnomad SAS

AF:

0.00289

Gnomad FIN

AF:

0.00669

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00523

Gnomad OTH

AF:

0.0177

GnomAD4 exome

AF:

0.00321

AC:

AN:

312

Hom.:

Cov.:

AF XY:

0.00435

AC XY:

AN XY:

230

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00370

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0238

AC:

3623

AN:

152324

Hom.:

110

Cov.:

AF XY:

0.0232

AC XY:

1728

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.0711

Gnomad4 AMR

AF:

0.0114

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.00174

Gnomad4 SAS

AF:

0.00290

Gnomad4 FIN

AF:

0.00669

Gnomad4 NFE

AF:

0.00523

Gnomad4 OTH

AF:

0.0175

Alfa

AF:

0.00598

Hom.:

Bravo

AF:

0.0277

Asia WGS

AF:

0.00375

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 26, 2015

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.0020

DANN

Benign

0.48

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