16-29876927-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001243332.2(SEZ6L2):c.1933C>T(p.Pro645Ser) 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. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001243332.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEZ6L2 | NM_001243332.2 | c.1933C>T | p.Pro645Ser | missense_variant | Exon 12 of 18 | ENST00000617533.5 | NP_001230261.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEZ6L2 | ENST00000617533.5 | c.1933C>T | p.Pro645Ser | missense_variant | Exon 12 of 18 | 1 | NM_001243332.2 | ENSP00000481917.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1457664Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 724414
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1933C>T (p.P645S) alteration is located in exon 12 (coding exon 12) of the SEZ6L2 gene. This alteration results from a C to T substitution at nucleotide position 1933, causing the proline (P) at amino acid position 645 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