1-154019012-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The ENST00000368559.8(NUP210L):c.4574C>G(p.Thr1525Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,613,916 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP210L | NM_207308.3 | c.4574C>G | p.Thr1525Ser | missense_variant | 33/40 | ENST00000368559.8 | |
NUP210L | XM_011510122.2 | c.4442C>G | p.Thr1481Ser | missense_variant | 32/39 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP210L | ENST00000368559.8 | c.4574C>G | p.Thr1525Ser | missense_variant | 33/40 | 5 | NM_207308.3 | P2 | |
NUP210L | ENST00000368553.5 | c.1373C>G | p.Thr458Ser | missense_variant | 11/16 | 1 | A2 | ||
NUP210L | ENST00000271854.3 | c.4574C>G | p.Thr1525Ser | missense_variant | 33/38 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249506Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135366
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461774Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727208
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2021 | The c.4574C>G (p.T1525S) alteration is located in exon 33 (coding exon 33) of the NUP210L gene. This alteration results from a C to G substitution at nucleotide position 4574, causing the threonine (T) at amino acid position 1525 to be replaced by a serine (S). 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