3-100744917-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006070.6(TFG):c.806G>A(p.Gly269Asp) variant causes a missense change. The variant allele was found at a frequency of 0.000000685 in 1,459,374 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
TFG
NM_006070.6 missense
NM_006070.6 missense
Scores
3
12
4
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.43
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TFG | NM_006070.6 | c.806G>A | p.Gly269Asp | missense_variant | 7/8 | ENST00000240851.9 | NP_006061.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TFG | ENST00000240851.9 | c.806G>A | p.Gly269Asp | missense_variant | 7/8 | 1 | NM_006070.6 | ENSP00000240851.4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250546Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135396
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GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459374Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726054
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
.;.;T;T;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
.;.;.;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D;D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;M;M;.;M
PrimateAI
Uncertain
T
PROVEAN
Benign
.;N;N;N;N;.
REVEL
Uncertain
Sift
Uncertain
.;D;D;D;D;.
Sift4G
Uncertain
T;D;T;T;D;T
Polyphen
0.95
.;.;P;P;.;.
Vest4
MutPred
Loss of glycosylation at P265 (P = 0.0107);.;Loss of glycosylation at P265 (P = 0.0107);Loss of glycosylation at P265 (P = 0.0107);.;Loss of glycosylation at P265 (P = 0.0107);
MVP
MPC
1.3
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at