chr11-108159003-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002519.3(NPAT):c.4223G>C(p.Ser1408Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S1408G) has been classified as Uncertain significance.
Frequency
Consequence
NM_002519.3 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 | UniProt |
---|---|---|---|---|---|---|---|
NPAT | NM_002519.3 | c.4223G>C | p.Ser1408Thr | missense_variant | 18/18 | ENST00000278612.9 | |
NPAT | NM_001321307.1 | c.4244G>C | p.Ser1415Thr | missense_variant | 18/18 | ||
NPAT | XM_011542854.3 | c.4250G>C | p.Ser1417Thr | missense_variant | 18/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPAT | ENST00000278612.9 | c.4223G>C | p.Ser1408Thr | missense_variant | 18/18 | 1 | NM_002519.3 | P1 | |
NPAT | ENST00000530859.1 | n.1596G>C | non_coding_transcript_exon_variant | 5/5 | 2 | ||||
NPAT | ENST00000530926.1 | n.380G>C | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000410 AC: 1AN: 243870Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132770
GnomAD4 exome Cov.: 27
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2022 | The p.S1408T variant (also known as c.4223G>C), located in coding exon 18 of the NPAT gene, results from a G to C substitution at nucleotide position 4223. The serine at codon 1408 is replaced by threonine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at