chr1-154009983-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The ENST00000368559.8(NUP210L):c.4919G>C(p.Ser1640Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,610,098 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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.4919G>C | p.Ser1640Thr | missense_variant | 35/40 | ENST00000368559.8 | |
NUP210L | XM_011510122.2 | c.4787G>C | p.Ser1596Thr | missense_variant | 34/39 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP210L | ENST00000368559.8 | c.4919G>C | p.Ser1640Thr | missense_variant | 35/40 | 5 | NM_207308.3 | P2 | |
NUP210L | ENST00000368553.5 | c.1718G>C | p.Ser573Thr | missense_variant | 13/16 | 1 | A2 | ||
NUP210L | ENST00000271854.3 | c.4919G>C | p.Ser1640Thr | missense_variant | 35/38 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152074Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 246592Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133740
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1458024Hom.: 0 Cov.: 30 AF XY: 0.0000248 AC XY: 18AN XY: 725120
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152074Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74252
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.4919G>C (p.S1640T) alteration is located in exon 35 (coding exon 35) of the NUP210L gene. This alteration results from a G to C substitution at nucleotide position 4919, causing the serine (S) at amino acid position 1640 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