rs6772054
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006070.6(TFG):āc.1090A>Cā(p.Thr364Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000817 in 1,614,106 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.0045 ( 7 hom., cov: 32)
Exomes š: 0.00044 ( 5 hom. )
Consequence
TFG
NM_006070.6 missense
NM_006070.6 missense
Scores
2
4
9
Clinical Significance
Conservation
PhyloP100: 8.34
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 Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0050143898).
BP6
?
Variant 3-100748418-A-C is Benign according to our data. Variant chr3-100748418-A-C is described in ClinVar as [Benign]. Clinvar id is 466404.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00447 (680/152266) while in subpopulation AFR AF= 0.0157 (651/41534). AF 95% confidence interval is 0.0147. There are 7 homozygotes in gnomad4. There are 313 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TFG | NM_006070.6 | c.1090A>C | p.Thr364Pro | missense_variant | 8/8 | ENST00000240851.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TFG | ENST00000240851.9 | c.1090A>C | p.Thr364Pro | missense_variant | 8/8 | 1 | NM_006070.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00446 AC: 678AN: 152148Hom.: 6 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00102 AC: 257AN: 251060Hom.: 5 AF XY: 0.000774 AC XY: 105AN XY: 135656
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GnomAD4 exome AF: 0.000437 AC: 639AN: 1461840Hom.: 5 Cov.: 33 AF XY: 0.000356 AC XY: 259AN XY: 727216
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GnomAD4 genome ? AF: 0.00447 AC: 680AN: 152266Hom.: 7 Cov.: 32 AF XY: 0.00420 AC XY: 313AN XY: 74462
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ESP6500AA
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ExAC
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161
Asia WGS
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3478
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 25, 2018 | - - |
Hereditary motor and sensory neuropathy, Okinawa type;C3714897:Hereditary spastic paraplegia 57 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Pathogenic
D;D;D;D
Sift4G
Benign
T;T;T;T
Polyphen
0.86
.;P;P;.
Vest4
MVP
MPC
0.88
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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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