rs138909849
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PVS1_ModeratePM2PP3_StrongPP5
The NM_014669.5(NUP93):c.1537+1G>A variant causes a splice donor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000395 in 1,518,982 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_014669.5 splice_donor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP93 | NM_014669.5 | c.1537+1G>A | splice_donor_variant | ENST00000308159.10 | |||
NUP93 | NM_001242795.2 | c.1168+1G>A | splice_donor_variant | ||||
NUP93 | NM_001242796.2 | c.1168+1G>A | splice_donor_variant | ||||
NUP93 | XM_005256263.4 | c.1537+1G>A | splice_donor_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP93 | ENST00000308159.10 | c.1537+1G>A | splice_donor_variant | 1 | NM_014669.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152222Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000293 AC: 4AN: 1366760Hom.: 0 Cov.: 31 AF XY: 0.00000297 AC XY: 2AN XY: 674374
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74374
ClinVar
Submissions by phenotype
Nephrotic syndrome, type 12 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 20, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at