16-29877325-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001243332.2(SEZ6L2):c.1855C>T(p.Pro619Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000428 in 1,612,620 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEZ6L2 | NM_001243332.2 | c.1855C>T | p.Pro619Ser | missense_variant | Exon 11 of 18 | ENST00000617533.5 | NP_001230261.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEZ6L2 | ENST00000617533.5 | c.1855C>T | p.Pro619Ser | missense_variant | Exon 11 of 18 | 1 | NM_001243332.2 | ENSP00000481917.1 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 246462Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 134006
GnomAD4 exome AF: 0.0000418 AC: 61AN: 1460380Hom.: 0 Cov.: 32 AF XY: 0.0000454 AC XY: 33AN XY: 726516
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1855C>T (p.P619S) alteration is located in exon 11 (coding exon 11) of the SEZ6L2 gene. This alteration results from a C to T substitution at nucleotide position 1855, causing the proline (P) at amino acid position 619 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