16-29877420-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001243332.2(SEZ6L2):c.1760G>A(p.Gly587Asp) variant causes a missense change. The variant allele was found at a frequency of 0.00000683 in 1,610,730 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEZ6L2 | NM_001243332.2 | c.1760G>A | p.Gly587Asp | 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.1760G>A | p.Gly587Asp | missense_variant | Exon 11 of 18 | 1 | NM_001243332.2 | ENSP00000481917.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152246Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 244362Hom.: 0 AF XY: 0.00000752 AC XY: 1AN XY: 132938
GnomAD4 exome AF: 0.00000549 AC: 8AN: 1458484Hom.: 0 Cov.: 32 AF XY: 0.00000689 AC XY: 5AN XY: 725534
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74396
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1760G>A (p.G587D) alteration is located in exon 11 (coding exon 11) of the SEZ6L2 gene. This alteration results from a G to A substitution at nucleotide position 1760, causing the glycine (G) at amino acid position 587 to be replaced by an aspartic acid (D). 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