chr17-74862937-T-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_024417.5(FDXR):c.1356A>G(p.Pro452=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00247 in 1,612,124 control chromosomes in the GnomAD database, including 79 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.013 ( 44 hom., cov: 34)
Exomes 𝑓: 0.0014 ( 35 hom. )
Consequence
FDXR
NM_024417.5 synonymous
NM_024417.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.59
Genes affected
FDXR (HGNC:3642): (ferredoxin reductase) This gene encodes a mitochondrial flavoprotein that initiates electron transport for cytochromes P450 receiving electrons from NADPH. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Apr 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 17-74862937-T-C is Benign according to our data. Variant chr17-74862937-T-C is described in ClinVar as [Benign]. Clinvar id is 785578.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0126 (1918/152346) while in subpopulation AFR AF= 0.0426 (1773/41578). AF 95% confidence interval is 0.041. There are 44 homozygotes in gnomad4. There are 911 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 45 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FDXR | NM_024417.5 | c.1356A>G | p.Pro452= | synonymous_variant | 12/12 | ENST00000293195.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FDXR | ENST00000293195.10 | c.1356A>G | p.Pro452= | synonymous_variant | 12/12 | 1 | NM_024417.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0125 AC: 1910AN: 152228Hom.: 45 Cov.: 34
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GnomAD3 exomes AF: 0.00325 AC: 809AN: 249136Hom.: 20 AF XY: 0.00226 AC XY: 306AN XY: 135118
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GnomAD4 exome AF: 0.00141 AC: 2063AN: 1459778Hom.: 35 Cov.: 29 AF XY: 0.00127 AC XY: 924AN XY: 726310
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
FDXR-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 30, 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -14
Find out detailed SpliceAI scores and Pangolin per-transcript scores at