rs516035

chr17-74866033-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024417.5(FDXR):c.507+98C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 1,019,088 control chromosomes in the GnomAD database, including 311,984 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.82 (51598 hom., cov: 31)
  • Exomes 𝑓: 0.77 (260386 hom.)
• Consequence: FDXR NM_024417.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FDXR	NM_024417.5	c.507+98C>A		intron_variant		ENST00000293195.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FDXR	ENST00000293195.10	c.507+98C>A		intron_variant		1	NM_024417.5	P3

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124313 AN: 151920 Hom.: 51540 Cov.: 31

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.797

GnomAD4 exome AF: 0.772 AC: 669578 AN: 867050 Hom.: 260386 AF XY: 0.772 AC XY: 344507 AN XY: 446424

Gnomad4 AFR exome AF: 0.948

Gnomad4 AMR exome AF: 0.854

Gnomad4 ASJ exome AF: 0.653

Gnomad4 EAS exome AF: 0.586

Gnomad4 SAS exome AF: 0.795

Gnomad4 FIN exome AF: 0.802

Gnomad4 NFE exome AF: 0.771

Gnomad4 OTH exome AF: 0.771

GnomAD4 genome AF: 0.818 AC: 124427 AN: 152038 Hom.: 51598 Cov.: 31 AF XY: 0.819 AC XY: 60855 AN XY: 74302

Gnomad4 AFR AF: 0.944

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.798

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.794

Alfa AF: 0.804 Hom.: 7841

Bravo AF: 0.822

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs516035; hg19: chr17-72862155;