chr1-154029954-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The ENST00000368559.8(NUP210L):c.3797G>C(p.Ser1266Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,716 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000368559.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP210L | NM_207308.3 | c.3797G>C | p.Ser1266Thr | missense_variant | 28/40 | ENST00000368559.8 | |
NUP210L | XM_011510122.2 | c.3665G>C | p.Ser1222Thr | missense_variant | 27/39 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP210L | ENST00000368559.8 | c.3797G>C | p.Ser1266Thr | missense_variant | 28/40 | 5 | NM_207308.3 | P2 | |
NUP210L | ENST00000368553.5 | c.596G>C | p.Ser199Thr | missense_variant | 6/16 | 1 | A2 | ||
NUP210L | ENST00000271854.3 | c.3797G>C | p.Ser1266Thr | missense_variant | 28/38 | 5 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459716Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726130
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 03, 2022 | The c.3797G>C (p.S1266T) alteration is located in exon 28 (coding exon 28) of the NUP210L gene. This alteration results from a G to C substitution at nucleotide position 3797, causing the serine (S) at amino acid position 1266 to be replaced by a threonine (T). 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
Publications
No publications associated with this variant yet.