chr1-229441977-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_018230.3(NUP133):c.3398G>T(p.Ser1133Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000125 in 1,594,242 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 (★).
Frequency
Consequence
NM_018230.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NUP133 | NM_018230.3 | c.3398G>T | p.Ser1133Ile | missense_variant | 26/26 | ENST00000261396.6 | NP_060700.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NUP133 | ENST00000261396.6 | c.3398G>T | p.Ser1133Ile | missense_variant | 26/26 | 1 | NM_018230.3 | ENSP00000261396 | P1 | |
NUP133 | ENST00000490352.1 | n.445G>T | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000431 AC: 1AN: 232130Hom.: 0 AF XY: 0.00000793 AC XY: 1AN XY: 126060
GnomAD4 exome AF: 6.94e-7 AC: 1AN: 1441898Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1AN XY: 717036
GnomAD4 genome AF: 0.00000656 AC: 1AN: 152344Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.3398G>T (p.S1133I) alteration is located in exon 26 (coding exon 26) of the NUP133 gene. This alteration results from a G to T substitution at nucleotide position 3398, causing the serine (S) at amino acid position 1133 to be replaced by an isoleucine (I). 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