9-69035900-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2 PP3 BS1_Supporting

The NM_000144.5(FXN):c.118C>T(p.Arg40Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000662 in 1,487,292 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00040 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00069 (1 hom.)
• Consequence: FXN NM_000144.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:3
• Conservation: PhyloP100: 0.0210

Genes affected

FXN (HGNC:3951): (frataxin) This nuclear gene encodes a mitochondrial protein which belongs to the FRATAXIN family. The protein functions in regulating mitochondrial iron transport and respiration. The expansion of intronic trinucleotide repeat GAA from 8-33 repeats to >90 repeats results in Friedreich ataxia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]

(HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.793
• BS1: Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.000692 (924/1335348) while in subpopulation NFE AF= 0.000842 (890/1057314). AF 95% confidence interval is 0.000795. There are 1 homozygotes in gnomad4_exome. There are 440 alleles in male gnomad4_exome subpopulation. Median coverage is 36. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FXN	NM_000144.5	c.118C>T	p.Arg40Cys	missense_variant	1/5	ENST00000484259.3
FXN	NM_181425.3	c.118C>T	p.Arg40Cys	missense_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FXN	ENST00000484259.3	c.118C>T	p.Arg40Cys	missense_variant	1/5	3	NM_000144.5	P1

Frequencies

GnomAD3 genomes AF: 0.000401 AC: 61 AN: 151944 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000262

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000780

Gnomad OTH AF: 0.000479

GnomAD3 exomes AF: 0.000299 AC: 27 AN: 90414 Hom.: 0 AF XY: 0.000255 AC XY: 13 AN XY: 50990

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000108

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000757

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000692 AC: 924 AN: 1335348 Hom.: 1 Cov.: 36 AF XY: 0.000668 AC XY: 440 AN XY: 658314

Gnomad4 AFR exome AF: 0.0000741

Gnomad4 AMR exome AF: 0.000166

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000134

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000842

Gnomad4 OTH exome AF: 0.000451

GnomAD4 genome AF: 0.000401 AC: 61 AN: 151944 Hom.: 0 Cov.: 33 AF XY: 0.000431 AC XY: 32 AN XY: 74206

Gnomad4 AFR AF: 0.0000483

Gnomad4 AMR AF: 0.000262

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000780

Gnomad4 OTH AF: 0.000479

Alfa AF: 0.000325 Hom.: 0

Bravo AF: 0.000427

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not specified Pathogenic:1 Uncertain:1

Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Mar 25, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 21, 2022	Variant summary: FXN c.118C>T (p.Arg40Cys) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00031 in 121496 control chromosomes (gnomAD). c.118C>T has been reported in the literature in the heterozygous state in an individual affected with hypertrophic cardiomyopathy (Van Driest_2005). However, this individual was also found carrying MYBPC3 c.2429G>A [p.Arg810His], which may have contributed to the patients' phenotype. Therefore, this report does not provide unequivocal conclusions about association of the variant with Friedreich Ataxia 1. Van Driest_2005 also provided experimental evidence demonstrating that the variant prevented the cleavage of the inactive-precursor form of frataxin to the active-mature form. However, when the investigators examined protein levels in patient fibroblasts, the levels of mature frataxin were similar to those seen in controls, not allowing for convincing conclusions about the variant effect. Three ClinVar submitters have assessed the variant since 2014: one classified the variant as pathogenic and two as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. -

Inborn genetic diseases Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 23, 2017

The p.R40C variant (also known as c.118C>T), located in coding exon 1 of the FXN gene, results from a C to T substitution at nucleotide position 118. The arginine at codon 40 is replaced by cysteine, an amino acid with highly dissimilar properties. This variant co-occurred with a missense alteration in MYBPC3 in a male patient diagnosed with hypertrophic cardiomyopathy at 12 years of age. The same group performed in vitro studies of the p.R40C variant and showed it was more sensitive to oxidative stress under metabolically demanding conditions; however, a skin biopsy from the patient mentioned above showed normal levels of frataxin mRNA and protein (Van Driest SL, Mol. Genet. Metab. 2005 Aug; 85(4):280-5). This amino acid position is well conserved on limited sequence alignment. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Hypertrophic cardiomyopathy Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Center for Advanced Laboratory Medicine, UC San Diego Health, University of California San Diego

Apr 18, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Uncertain	0.039	T
BayesDel_noAF	Pathogenic	0.18
Cadd	Benign	20
Dann	Uncertain	1.0
DEOGEN2	Uncertain	0.47	T;.;.;T;.;.
Eigen	Benign	-0.31
Eigen_PC	Benign	-0.55
FATHMM_MKL	Benign	0.10	N
M_CAP	Pathogenic	0.77	D
MetaRNN	Pathogenic	0.79	D;D;D;D;D;D
MetaSVM	Uncertain	0.51	D
MutationAssessor	Benign	1.9	L;L;L;L;.;.
MutationTaster	Benign	7.6e-8	A;A;A
PrimateAI	Uncertain	0.59	T
Polyphen		0.99	D;D;.;D;.;.
Vest4		0.27, 0.33
MVP		0.95
ClinPred		0.19	T
GERP RS		2.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Varity_R		0.12
gMVP		0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs145854903; hg19: chr9-71650816;