rs552432

chr17-74864131-G-Achr17-74864131-G-Cchr17-74864131-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.1002+17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 1,612,686 control chromosomes in the GnomAD database, including 448,150 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 0.74 (42069 hom., cov: 32)
  • Exomes 𝑓: 0.74 (406081 hom.)
• Consequence: FDXR NM_024417.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FDXR	NM_024417.5	c.1002+17C>T		intron_variant		ENST00000293195.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FDXR	ENST00000293195.10	c.1002+17C>T		intron_variant		1	NM_024417.5	P3

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112617 AN: 151968 Hom.: 42047 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.733

GnomAD4 exome AF: 0.744 AC: 1085956 AN: 1460598 Hom.: 406081 Cov.: 56 AF XY: 0.744 AC XY: 540433 AN XY: 726568

Gnomad4 AFR exome AF: 0.741

Gnomad4 AMR exome AF: 0.834

Gnomad4 ASJ exome AF: 0.623

Gnomad4 EAS exome AF: 0.510

Gnomad4 SAS exome AF: 0.769

Gnomad4 FIN exome AF: 0.758

Gnomad4 NFE exome AF: 0.749

Gnomad4 OTH exome AF: 0.731

GnomAD4 genome AF: 0.741 AC: 112686 AN: 152088 Hom.: 42069 Cov.: 32 AF XY: 0.742 AC XY: 55196 AN XY: 74358

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.794

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.730

Alfa AF: 0.705 Hom.: 5260

Bravo AF: 0.740

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	16
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs552432; hg19: chr17-72860253;