chr9-130904075-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032843.5(FIBCD1):c.1375G>A(p.Glu459Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000000685 in 1,460,368 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_032843.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FIBCD1 | NM_032843.5 | c.1375G>A | p.Glu459Lys | missense_variant | Exon 7 of 7 | ENST00000372338.9 | NP_116232.3 | |
FIBCD1 | NM_001145106.2 | c.1375G>A | p.Glu459Lys | missense_variant | Exon 8 of 8 | NP_001138578.1 | ||
FIBCD1 | XM_047423989.1 | c.1375G>A | p.Glu459Lys | missense_variant | Exon 8 of 8 | XP_047279945.1 | ||
FIBCD1 | XM_047423990.1 | c.901G>A | p.Glu301Lys | missense_variant | Exon 7 of 7 | XP_047279946.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FIBCD1 | ENST00000372338.9 | c.1375G>A | p.Glu459Lys | missense_variant | Exon 7 of 7 | 1 | NM_032843.5 | ENSP00000361413.4 | ||
FIBCD1 | ENST00000448616.5 | c.1375G>A | p.Glu459Lys | missense_variant | Exon 8 of 8 | 5 | ENSP00000414501.1 | |||
FIBCD1 | ENST00000372337.6 | c.901G>A | p.Glu301Lys | missense_variant | Exon 7 of 7 | 5 | ENSP00000361412.1 | |||
FIBCD1 | ENST00000444139.5 | c.806-3G>A | splice_region_variant, intron_variant | Intron 4 of 4 | 2 | ENSP00000395319.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 246830Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134604
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460368Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726462
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1375G>A (p.E459K) alteration is located in exon 7 (coding exon 7) of the FIBCD1 gene. This alteration results from a G to A substitution at nucleotide position 1375, causing the glutamic acid (E) at amino acid position 459 to be replaced by a lysine (K). 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