9-134883307-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004108.3(FCN2):c.220C>T(p.Arg74Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000639 in 1,612,908 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R74H) has been classified as Uncertain significance.
Frequency
Consequence
NM_004108.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FCN2 | NM_004108.3 | c.220C>T | p.Arg74Cys | missense_variant | 3/8 | ENST00000291744.11 | |
FCN2 | NM_015837.3 | c.106C>T | p.Arg36Cys | missense_variant | 2/7 | ||
FCN2 | XM_011518392.4 | c.187C>T | p.Arg63Cys | missense_variant | 3/8 | ||
FCN2 | XM_006717015.5 | c.73C>T | p.Arg25Cys | missense_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCN2 | ENST00000291744.11 | c.220C>T | p.Arg74Cys | missense_variant | 3/8 | 1 | NM_004108.3 | P1 | |
FCN2 | ENST00000350339.3 | c.106C>T | p.Arg36Cys | missense_variant | 2/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152150Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251002Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135764
GnomAD4 exome AF: 0.0000644 AC: 94AN: 1460758Hom.: 0 Cov.: 33 AF XY: 0.0000578 AC XY: 42AN XY: 726760
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152150Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.220C>T (p.R74C) alteration is located in exon 3 (coding exon 3) of the FCN2 gene. This alteration results from a C to T substitution at nucleotide position 220, causing the arginine (R) at amino acid position 74 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at