rs1553154186
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP2
The NM_001365999.1(SZT2):c.8182G>C(p.Glu2728Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,458,768 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. E2728E) has been classified as Likely benign.
Frequency
Consequence
NM_001365999.1 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 |
---|---|---|---|---|---|---|---|
SZT2 | NM_001365999.1 | c.8182G>C | p.Glu2728Gln | missense_variant | 59/72 | ENST00000634258.3 | |
SZT2 | NM_015284.4 | c.8011G>C | p.Glu2671Gln | missense_variant | 58/71 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SZT2 | ENST00000634258.3 | c.8182G>C | p.Glu2728Gln | missense_variant | 59/72 | 5 | NM_001365999.1 | P1 | |
SZT2 | ENST00000562955.2 | c.8011G>C | p.Glu2671Gln | missense_variant | 58/71 | 5 | |||
SZT2 | ENST00000648058.1 | n.4636G>C | non_coding_transcript_exon_variant | 27/40 | |||||
SZT2 | ENST00000649403.1 | n.2932G>C | non_coding_transcript_exon_variant | 24/37 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1458768Hom.: 0 Cov.: 36 AF XY: 0.00000276 AC XY: 2AN XY: 725484
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 28, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at