chr12-108518522-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_007076.3(FICD):c.424G>A(p.Ala142Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,614,164 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. A142V) has been classified 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FICD | NM_007076.3 | c.424G>A | p.Ala142Thr | missense_variant | 3/3 | ENST00000552695.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FICD | ENST00000552695.6 | c.424G>A | p.Ala142Thr | missense_variant | 3/3 | 1 | NM_007076.3 | P1 | |
FICD | ENST00000361549.2 | c.*161G>A | 3_prime_UTR_variant | 3/3 | 1 | ||||
FICD | ENST00000549641.1 | c.153+1249G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251490Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135920
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461884Hom.: 0 Cov.: 33 AF XY: 0.0000248 AC XY: 18AN XY: 727244
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2023 | The c.424G>A (p.A142T) alteration is located in exon 3 (coding exon 2) of the FICD gene. This alteration results from a G to A substitution at nucleotide position 424, causing the alanine (A) at amino acid position 142 to be replaced by a threonine (T). 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