rs80338889
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 4P and 2B. PM2PM5BP4_Moderate
The NM_003227.4(TFR2):c.2069A>G(p.Gln690Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,176 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q690P) has been classified as Pathogenic.
Frequency
Consequence
NM_003227.4 missense
Scores
Clinical Significance
Conservation
Publications
- hemochromatosis type 3Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet, Genomics England PanelApp, G2P
Genome browser will be placed here
ACMG classification
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TFR2 | NM_003227.4 | c.2069A>G | p.Gln690Arg | missense_variant | Exon 17 of 18 | ENST00000223051.8 | NP_003218.2 | |
TFR2 | NM_001206855.3 | c.1556A>G | p.Gln519Arg | missense_variant | Exon 14 of 15 | NP_001193784.1 | ||
LOC124901709 | XR_007060454.1 | n.433+4276T>C | intron_variant | Intron 1 of 2 | ||||
LOC124901710 | XR_007060455.1 | n.-80A>G | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 33 show subpopulations
GnomAD4 exome Cov.: 36
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74334 show subpopulations
Age Distribution
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at