rs2239641
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001128148.3(TFRC):c.1468+39A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 1,574,680 control chromosomes in the GnomAD database, including 264,268 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.48 ( 19438 hom., cov: 33)
Exomes 𝑓: 0.58 ( 244830 hom. )
Consequence
TFRC
NM_001128148.3 intron
NM_001128148.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.500
Genes affected
TFRC (HGNC:11763): (transferrin receptor) This gene encodes a cell surface receptor necessary for cellular iron uptake by the process of receptor-mediated endocytosis. This receptor is required for erythropoiesis and neurologic development. Multiple alternatively spliced variants have been identified. [provided by RefSeq, Sep 2015]
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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=-0.8).
BP6
?
Variant 3-196062543-T-C is Benign according to our data. Variant chr3-196062543-T-C is described in ClinVar as [Benign]. Clinvar id is 1273355.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TFRC | NM_001128148.3 | c.1468+39A>G | intron_variant | ENST00000360110.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TFRC | ENST00000360110.9 | c.1468+39A>G | intron_variant | 1 | NM_001128148.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.482 AC: 73313AN: 152050Hom.: 19441 Cov.: 33
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GnomAD3 exomes AF: 0.503 AC: 119475AN: 237402Hom.: 32722 AF XY: 0.515 AC XY: 66380AN XY: 128920
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GnomAD4 exome AF: 0.578 AC: 822548AN: 1422512Hom.: 244830 Cov.: 24 AF XY: 0.578 AC XY: 410071AN XY: 709408
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GnomAD4 genome ? AF: 0.482 AC: 73322AN: 152168Hom.: 19438 Cov.: 33 AF XY: 0.478 AC XY: 35541AN XY: 74386
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 12, 2023 | This variant is classified as Benign based on local population frequency. This variant was detected in 65% of patients studied by a panel of primary immunodeficiencies. Number of patients: 62. Only high quality variants are reported. - |
TFRC-related combined immunodeficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 10, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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