13-28138919-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_175854.8(PAN3):c.262C>G(p.Leu88Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000293 in 1,363,750 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_175854.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAN3 | ENST00000380958.8 | c.262C>G | p.Leu88Val | missense_variant | Exon 1 of 19 | 5 | NM_175854.8 | ENSP00000370345.3 | ||
PAN3 | ENST00000503791.5 | n.414C>G | non_coding_transcript_exon_variant | Exon 1 of 14 | 2 | |||||
PAN3 | ENST00000399613.1 | c.-177C>G | upstream_gene_variant | 5 | ENSP00000382522.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152012Hom.: 1 Cov.: 30
GnomAD4 exome AF: 8.25e-7 AC: 1AN: 1211738Hom.: 0 Cov.: 33 AF XY: 0.00000170 AC XY: 1AN XY: 588052
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152012Hom.: 1 Cov.: 30 AF XY: 0.0000404 AC XY: 3AN XY: 74234
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.262C>G (p.L88V) alteration is located in exon 1 (coding exon 1) of the PAN3 gene. This alteration results from a C to G substitution at nucleotide position 262, causing the leucine (L) at amino acid position 88 to be replaced by a valine (V). 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