12-68690618-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001330192.2(NUP107):c.88C>A(p.Leu30Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,614,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001330192.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NUP107 | NM_020401.4 | c.188-13C>A | intron_variant | Intron 3 of 27 | ENST00000229179.9 | NP_065134.1 | ||
NUP107 | NM_001330192.2 | c.88C>A | p.Leu30Ile | missense_variant | Exon 4 of 28 | NP_001317121.1 | ||
NUP107 | XM_005269037.5 | c.188-13C>A | intron_variant | Intron 3 of 26 | XP_005269094.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152114Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251276Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135800
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461804Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727216
GnomAD4 genome AF: 0.000171 AC: 26AN: 152232Hom.: 0 Cov.: 31 AF XY: 0.000228 AC XY: 17AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at