7-135571246-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001329434.2(NUP205):c.-916C>T variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.0000187 in 1,387,392 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001329434.2 5_prime_UTR_premature_start_codon_gain
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NUP205 | NM_015135.3 | c.170C>T | p.Pro57Leu | missense_variant, splice_region_variant | Exon 2 of 43 | ENST00000285968.11 | NP_055950.2 | |
NUP205 | NM_001329434.2 | c.-916C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 43 | NP_001316363.2 | |||
NUP205 | NM_001329434.2 | c.-916C>T | splice_region_variant | Exon 2 of 43 | NP_001316363.2 | |||
NUP205 | NM_001329434.2 | c.-916C>T | 5_prime_UTR_variant | Exon 2 of 43 | NP_001316363.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NUP205 | ENST00000285968.11 | c.170C>T | p.Pro57Leu | missense_variant, splice_region_variant | Exon 2 of 43 | 1 | NM_015135.3 | ENSP00000285968.6 | ||
NUP205 | ENST00000489493.1 | n.425C>T | splice_region_variant, non_coding_transcript_exon_variant | Exon 2 of 3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000134 AC: 2AN: 149466Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000572 AC: 9AN: 157260Hom.: 0 AF XY: 0.0000569 AC XY: 5AN XY: 87914
GnomAD4 exome AF: 0.0000194 AC: 24AN: 1237926Hom.: 0 Cov.: 29 AF XY: 0.0000132 AC XY: 8AN XY: 604356
GnomAD4 genome AF: 0.0000134 AC: 2AN: 149466Hom.: 0 Cov.: 29 AF XY: 0.0000137 AC XY: 1AN XY: 72836
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 57 of the NUP205 protein (p.Pro57Leu). This variant is present in population databases (rs369458508, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with NUP205-related conditions. ClinVar contains an entry for this variant (Variation ID: 1449439). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at