chr12-108517038-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007076.3(FICD):c.66C>G(p.Ser22Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000152 in 1,582,104 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007076.3 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 |
---|---|---|---|---|---|---|---|
FICD | NM_007076.3 | c.66C>G | p.Ser22Arg | missense_variant | 2/3 | ENST00000552695.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FICD | ENST00000552695.6 | c.66C>G | p.Ser22Arg | missense_variant | 2/3 | 1 | NM_007076.3 | P1 | |
FICD | ENST00000361549.2 | c.66C>G | p.Ser22Arg | missense_variant | 2/3 | 1 | |||
FICD | ENST00000552758.1 | c.66C>G | p.Ser22Arg | missense_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000214 AC: 5AN: 233550Hom.: 0 AF XY: 0.0000395 AC XY: 5AN XY: 126614
GnomAD4 exome AF: 0.0000133 AC: 19AN: 1429850Hom.: 0 Cov.: 31 AF XY: 0.0000183 AC XY: 13AN XY: 709188
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2023 | The c.66C>G (p.S22R) alteration is located in exon 2 (coding exon 1) of the FICD gene. This alteration results from a C to G substitution at nucleotide position 66, causing the serine (S) at amino acid position 22 to be replaced by an arginine (R). 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