12-68689598-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020401.4(NUP107):c.166C>T(p.Pro56Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,610,594 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020401.4 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 |
---|---|---|---|---|---|---|---|---|
NUP107 | NM_020401.4 | c.166C>T | p.Pro56Ser | missense_variant | Exon 3 of 28 | ENST00000229179.9 | NP_065134.1 | |
NUP107 | XM_005269037.5 | c.166C>T | p.Pro56Ser | missense_variant | Exon 3 of 27 | XP_005269094.1 | ||
NUP107 | NM_001330192.2 | c.51C>T | p.Leu17Leu | synonymous_variant | Exon 3 of 28 | NP_001317121.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1458448Hom.: 0 Cov.: 29 AF XY: 0.00000414 AC XY: 3AN XY: 725440
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74320
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.166C>T (p.P56S) alteration is located in exon 3 (coding exon 3) of the NUP107 gene. This alteration results from a C to T substitution at nucleotide position 166, causing the proline (P) at amino acid position 56 to be replaced by a serine (S). 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