rs8177220
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001063.4(TF):c.502+110G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00121 in 1,213,600 control chromosomes in the GnomAD database, including 13 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 0.0016 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 11 hom. )
Consequence
TF
NM_001063.4 intron
NM_001063.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.213
Genes affected
TF (HGNC:11740): (transferrin) This gene encodes a glycoprotein with an approximate molecular weight of 76.5 kDa. It is thought to have been created as a result of an ancient gene duplication event that led to generation of homologous C and N-terminal domains each of which binds one ion of ferric iron. The function of this protein is to transport iron from the intestine, reticuloendothelial system, and liver parenchymal cells to all proliferating cells in the body. This protein may also have a physiologic role as granulocyte/pollen-binding protein (GPBP) involved in the removal of certain organic matter and allergens from serum. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TF | NM_001063.4 | c.502+110G>C | intron_variant | ENST00000402696.9 | NP_001054.2 | |||
TF | NM_001354703.2 | c.370+110G>C | intron_variant | NP_001341632.2 | ||||
TF | NM_001354704.2 | c.121+110G>C | intron_variant | NP_001341633.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TF | ENST00000402696.9 | c.502+110G>C | intron_variant | 1 | NM_001063.4 | ENSP00000385834.3 |
Frequencies
GnomAD3 genomes AF: 0.00158 AC: 240AN: 152198Hom.: 2 Cov.: 32
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GnomAD4 exome AF: 0.00116 AC: 1227AN: 1061284Hom.: 11 AF XY: 0.00109 AC XY: 593AN XY: 545412
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GnomAD4 genome AF: 0.00158 AC: 240AN: 152316Hom.: 2 Cov.: 32 AF XY: 0.00222 AC XY: 165AN XY: 74480
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at