chr17-74862879-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_024417.5(FDXR):c.1414A>G(p.Thr472Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00561 in 1,613,208 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_024417.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FDXR | NM_024417.5 | c.1414A>G | p.Thr472Ala | missense_variant | 12/12 | ENST00000293195.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FDXR | ENST00000293195.10 | c.1414A>G | p.Thr472Ala | missense_variant | 12/12 | 1 | NM_024417.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00458 AC: 697AN: 152174Hom.: 2 Cov.: 34
GnomAD3 exomes AF: 0.00441 AC: 1105AN: 250362Hom.: 5 AF XY: 0.00458 AC XY: 621AN XY: 135588
GnomAD4 exome AF: 0.00571 AC: 8347AN: 1460916Hom.: 29 Cov.: 29 AF XY: 0.00576 AC XY: 4187AN XY: 726804
GnomAD4 genome ? AF: 0.00458 AC: 697AN: 152292Hom.: 2 Cov.: 34 AF XY: 0.00414 AC XY: 308AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | FDXR: BP4, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
FDXR-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 07, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at