1-153995151-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_207308.3(NUP210L):c.5416C>T(p.Arg1806Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,678 control chromosomes in the GnomAD database, including 1 homozygotes. 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
NM_207308.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NUP210L | NM_207308.3 | c.5416C>T | p.Arg1806Trp | missense_variant | 38/40 | NP_997191.2 | ||
NUP210L | NM_001159484.1 | c.4960C>T | p.Arg1654Trp | missense_variant | 36/38 | NP_001152956.1 | ||
NUP210L | XM_011510122.2 | c.5284C>T | p.Arg1762Trp | missense_variant | 37/39 | XP_011508424.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NUP210L | ENST00000368559.8 | c.5416C>T | p.Arg1806Trp | missense_variant | 38/40 | 5 | ENSP00000357547.3 | |||
NUP210L | ENST00000368553.5 | c.1759C>T | p.Arg587Trp | missense_variant | 14/16 | 1 | ENSP00000357541.1 | |||
NUP210L | ENST00000271854.3 | c.4960C>T | p.Arg1654Trp | missense_variant | 36/38 | 5 | ENSP00000271854.3 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152126Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249536Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135386
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461552Hom.: 1 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727116
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152126Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2023 | The c.5416C>T (p.R1806W) alteration is located in exon 38 (coding exon 38) of the NUP210L gene. This alteration results from a C to T substitution at nucleotide position 5416, causing the arginine (R) at amino acid position 1806 to be replaced by a tryptophan (W). 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