chr9-134885882-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004108.3(FCN2):c.544G>T(p.Ala182Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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.544G>T | p.Ala182Ser | missense_variant | 6/8 | ENST00000291744.11 | |
FCN2 | NM_015837.3 | c.430G>T | p.Ala144Ser | missense_variant | 5/7 | ||
FCN2 | XM_011518392.4 | c.511G>T | p.Ala171Ser | missense_variant | 6/8 | ||
FCN2 | XM_006717015.5 | c.397G>T | p.Ala133Ser | missense_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCN2 | ENST00000291744.11 | c.544G>T | p.Ala182Ser | missense_variant | 6/8 | 1 | NM_004108.3 | P1 | |
FCN2 | ENST00000350339.3 | c.430G>T | p.Ala144Ser | missense_variant | 5/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000461 AC: 7AN: 151966Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249348Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134926
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461076Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 726836
GnomAD4 genome ? AF: 0.0000461 AC: 7AN: 151966Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74182
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2022 | The c.544G>T (p.A182S) alteration is located in exon 6 (coding exon 6) of the FCN2 gene. This alteration results from a G to T substitution at nucleotide position 544, causing the alanine (A) at amino acid position 182 to be replaced by a serine (S). 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