chr17-74863142-C-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_024417.5(FDXR):c.1279G>T(p.Ala427Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000561 in 1,613,788 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_024417.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FDXR | NM_024417.5 | c.1279G>T | p.Ala427Ser | missense_variant | 11/12 | ENST00000293195.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FDXR | ENST00000293195.10 | c.1279G>T | p.Ala427Ser | missense_variant | 11/12 | 1 | NM_024417.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00274 AC: 417AN: 152258Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.000797 AC: 199AN: 249648Hom.: 1 AF XY: 0.000621 AC XY: 84AN XY: 135322
GnomAD4 exome AF: 0.000330 AC: 482AN: 1461412Hom.: 4 Cov.: 35 AF XY: 0.000282 AC XY: 205AN XY: 726996
GnomAD4 genome ? AF: 0.00278 AC: 424AN: 152376Hom.: 1 Cov.: 34 AF XY: 0.00248 AC XY: 185AN XY: 74522
ClinVar
Submissions by phenotype
FDXR-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 31, 2021 | 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | FDXR: BP4, BS1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at