chr7-100627386-G-GCTGGGCCACGGC
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_003227.4(TFR2):c.1872_1873insGCCGTGGCCCAG(p.Ala621_Gln624dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000385 in 1,559,462 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: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000036 ( 0 hom. )
Consequence
TFR2
NM_003227.4 inframe_insertion
NM_003227.4 inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.598
Genes affected
TFR2 (HGNC:11762): (transferrin receptor 2) This gene encodes a single-pass type II membrane protein, which is a member of the transferrin receptor-like family. This protein mediates cellular uptake of transferrin-bound iron, and may be involved in iron metabolism, hepatocyte function and erythrocyte differentiation. Mutations in this gene have been associated with hereditary hemochromatosis type III. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, May 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_003227.4.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TFR2 | NM_003227.4 | c.1872_1873insGCCGTGGCCCAG | p.Ala621_Gln624dup | inframe_insertion | 16/18 | ENST00000223051.8 | |
LOC124901709 | XR_007060454.1 | n.434-3757_434-3746dup | intron_variant, non_coding_transcript_variant | ||||
TFR2 | NM_001206855.3 | c.1359_1360insGCCGTGGCCCAG | p.Ala450_Gln453dup | inframe_insertion | 13/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TFR2 | ENST00000223051.8 | c.1872_1873insGCCGTGGCCCAG | p.Ala621_Gln624dup | inframe_insertion | 16/18 | 1 | NM_003227.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.00000355 AC: 5AN: 1407252Hom.: 0 Cov.: 35 AF XY: 0.00000288 AC XY: 2AN XY: 694998
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74338
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at