22-26292655-C-G
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_021115.5(SEZ6L):c.344C>G(p.Pro115Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000917 in 1,613,300 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 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. P115L) has been classified as Uncertain significance.
Frequency
Consequence
NM_021115.5 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000467 AC: 71AN: 152164Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000112 AC: 28AN: 249110 AF XY: 0.0000668 show subpopulations
GnomAD4 exome AF: 0.0000527 AC: 77AN: 1461018Hom.: 0 Cov.: 32 AF XY: 0.0000413 AC XY: 30AN XY: 726820 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000466 AC: 71AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.000416 AC XY: 31AN XY: 74452 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.344C>G (p.P115R) alteration is located in exon 2 (coding exon 2) of the SEZ6L gene. This alteration results from a C to G substitution at nucleotide position 344, causing the proline (P) at amino acid position 115 to be replaced by an arginine (R). 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