12-68689542-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_020401.4(NUP107):c.110C>T(p.Ser37Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000871 in 1,606,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP107 | NM_020401.4 | c.110C>T | p.Ser37Phe | missense_variant | 3/28 | ENST00000229179.9 | |
NUP107 | XM_005269037.5 | c.110C>T | p.Ser37Phe | missense_variant | 3/27 | ||
NUP107 | NM_001330192.2 | c.-6C>T | 5_prime_UTR_variant | 3/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP107 | ENST00000229179.9 | c.110C>T | p.Ser37Phe | missense_variant | 3/28 | 1 | NM_020401.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000807 AC: 2AN: 247804Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134038
GnomAD4 exome AF: 0.00000756 AC: 11AN: 1454674Hom.: 0 Cov.: 28 AF XY: 0.00000829 AC XY: 6AN XY: 723996
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152302Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74470
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 17, 2024 | The c.110C>T (p.S37F) alteration is located in exon 3 (coding exon 3) of the NUP107 gene. This alteration results from a C to T substitution at nucleotide position 110, causing the serine (S) at amino acid position 37 to be replaced by a phenylalanine (F). 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