7-100626830-T-G
Variant summary
Our verdict is Likely pathogenic. The variant received 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_003227.4(TFR2):c.2069A>C(p.Gln690Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000429 in 1,397,372 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
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
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ACMG classification
Our verdict: Likely_pathogenic. The variant received 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TFR2 | NM_003227.4 | c.2069A>C | p.Gln690Pro | missense_variant | Exon 17 of 18 | ENST00000223051.8 | NP_003218.2 | |
TFR2 | NM_001206855.3 | c.1556A>C | p.Gln519Pro | missense_variant | Exon 14 of 15 | NP_001193784.1 | ||
LOC124901709 | XR_007060454.1 | n.433+4276T>G | intron_variant | Intron 1 of 2 | ||||
LOC124901710 | XR_007060455.1 | n.-80A>C | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000429 AC: 6AN: 1397372Hom.: 0 Cov.: 36 AF XY: 0.00000580 AC XY: 4AN XY: 689376 show subpopulations
Age Distribution
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Hemochromatosis type 3 Pathogenic:1Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at