chr12-68689015-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020401.4(NUP107):c.62G>A(p.Arg21Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000229 in 1,613,416 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 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. R21W) 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.62G>A | p.Arg21Gln | missense_variant | 2/28 | ENST00000229179.9 | |
NUP107 | XM_005269037.5 | c.62G>A | p.Arg21Gln | missense_variant | 2/27 | ||
NUP107 | NM_001330192.2 | c.-54G>A | 5_prime_UTR_variant | 2/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP107 | ENST00000229179.9 | c.62G>A | p.Arg21Gln | missense_variant | 2/28 | 1 | NM_020401.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251074Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135702
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461282Hom.: 0 Cov.: 29 AF XY: 0.0000303 AC XY: 22AN XY: 726972
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74306
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2022 | The c.62G>A (p.R21Q) alteration is located in exon 2 (coding exon 2) of the NUP107 gene. This alteration results from a G to A substitution at nucleotide position 62, causing the arginine (R) at amino acid position 21 to be replaced by a glutamine (Q). 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