chr1-27370933-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003665.4(FCN3):c.433C>T(p.Arg145Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,613,658 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003665.4 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 |
---|---|---|---|---|---|---|---|
FCN3 | NM_003665.4 | c.433C>T | p.Arg145Cys | missense_variant | 6/8 | ENST00000270879.9 | |
FCN3 | NM_173452.3 | c.400C>T | p.Arg134Cys | missense_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCN3 | ENST00000270879.9 | c.433C>T | p.Arg145Cys | missense_variant | 6/8 | 1 | NM_003665.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 152066Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250728Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135630
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461474Hom.: 0 Cov.: 32 AF XY: 0.0000206 AC XY: 15AN XY: 727016
GnomAD4 genome ? AF: 0.000171 AC: 26AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74412
ClinVar
Submissions by phenotype
FCN3-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 08, 2023 | The FCN3 c.433C>T variant is predicted to result in the amino acid substitution p.Arg145Cys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.036% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-27697424-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at