chr7-100620917-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_003227.4(TFR2):c.2346G>A(p.Thr782=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,613,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T782T) has been classified as Likely benign.
Frequency
Consequence
NM_003227.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TFR2 | NM_003227.4 | c.2346G>A | p.Thr782= | synonymous_variant | 18/18 | ENST00000223051.8 | |
TFR2 | NM_001206855.3 | c.1833G>A | p.Thr611= | synonymous_variant | 15/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TFR2 | ENST00000223051.8 | c.2346G>A | p.Thr782= | synonymous_variant | 18/18 | 1 | NM_003227.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000559 AC: 14AN: 250618Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135530
GnomAD4 exome AF: 0.0000369 AC: 54AN: 1461726Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727120
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74368
ClinVar
Submissions by phenotype
Hemochromatosis type 3 Benign:1
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Apr 16, 2020 | - - |
Hereditary hemochromatosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 28, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at