chr12-68689014-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.61C>T(p.Arg21Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000446 in 1,613,560 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R21Q) has been classified 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP107 | NM_020401.4 | c.61C>T | p.Arg21Trp | missense_variant | 2/28 | ENST00000229179.9 | |
NUP107 | XM_005269037.5 | c.61C>T | p.Arg21Trp | missense_variant | 2/27 | ||
NUP107 | NM_001330192.2 | c.-55C>T | 5_prime_UTR_variant | 2/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP107 | ENST00000229179.9 | c.61C>T | p.Arg21Trp | missense_variant | 2/28 | 1 | NM_020401.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251102Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135706
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461316Hom.: 0 Cov.: 29 AF XY: 0.0000426 AC XY: 31AN XY: 726972
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74420
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 17, 2022 | The c.61C>T (p.R21W) alteration is located in exon 2 (coding exon 2) of the NUP107 gene. This alteration results from a C to T substitution at nucleotide position 61, causing the arginine (R) at amino acid position 21 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Premature ovarian insufficiency Uncertain:1
Uncertain significance, no assertion criteria provided | research | Reproductive Development, Murdoch Childrens Research Institute | Jan 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at