1-229508126-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018230.3(NUP133):c.124G>A(p.Ala42Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000442 in 1,584,586 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A42V) has been classified as Uncertain significance.
Frequency
Consequence
NM_018230.3 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 |
---|---|---|---|---|---|---|---|---|---|---|
NUP133 | ENST00000261396.6 | c.124G>A | p.Ala42Thr | missense_variant | Exon 1 of 26 | 1 | NM_018230.3 | ENSP00000261396.3 | ||
NUP133 | ENST00000366678.4 | n.201G>A | non_coding_transcript_exon_variant | Exon 1 of 6 | 5 | |||||
NUP133-DT | ENST00000417605.2 | n.-243C>T | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000898 AC: 2AN: 222768Hom.: 0 AF XY: 0.00000811 AC XY: 1AN XY: 123234
GnomAD4 exome AF: 0.00000349 AC: 5AN: 1432364Hom.: 0 Cov.: 31 AF XY: 0.00000422 AC XY: 3AN XY: 711618
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.124G>A (p.A42T) alteration is located in exon 1 (coding exon 1) of the NUP133 gene. This alteration results from a G to A substitution at nucleotide position 124, causing the alanine (A) at amino acid position 42 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