chr1-74201361-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003838.5(FPGT):āc.294G>Cā(p.Lys98Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,611,752 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 (ā ).
Frequency
Consequence
NM_003838.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FPGT | NM_003838.5 | c.294G>C | p.Lys98Asn | missense_variant | 3/4 | ENST00000370898.9 | |
FPGT-TNNI3K | NM_001112808.3 | c.294G>C | p.Lys98Asn | missense_variant | 3/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FPGT | ENST00000370898.9 | c.294G>C | p.Lys98Asn | missense_variant | 3/4 | 1 | NM_003838.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152132Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247502Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134052
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1459620Hom.: 0 Cov.: 29 AF XY: 0.0000234 AC XY: 17AN XY: 726182
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152132Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2023 | The c.294G>C (p.K98N) alteration is located in exon 3 (coding exon 3) of the FPGT gene. This alteration results from a G to C substitution at nucleotide position 294, causing the lysine (K) at amino acid position 98 to be replaced by an asparagine (N). 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