chr17-28958132-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_178860.5(SEZ6):c.2117G>A(p.Arg706His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000754 in 1,592,246 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R706C) has been classified as Uncertain significance.
Frequency
Consequence
NM_178860.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEZ6 | NM_178860.5 | c.2117G>A | p.Arg706His | missense_variant | 11/17 | ENST00000317338.17 | |
LOC105371716 | XR_001752822.2 | n.1807+4724C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEZ6 | ENST00000317338.17 | c.2117G>A | p.Arg706His | missense_variant | 11/17 | 1 | NM_178860.5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 244182Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132442
GnomAD4 exome AF: 0.00000556 AC: 8AN: 1440070Hom.: 0 Cov.: 31 AF XY: 0.00000703 AC XY: 5AN XY: 711736
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2021 | The c.2117G>A (p.R706H) alteration is located in exon 11 (coding exon 11) of the SEZ6 gene. This alteration results from a G to A substitution at nucleotide position 2117, causing the arginine (R) at amino acid position 706 to be replaced by a histidine (H). 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