1-43445992-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001365999.1(SZT2):c.8916+8G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 1,613,566 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001365999.1 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SZT2 | NM_001365999.1 | c.8916+8G>A | splice_region_variant, intron_variant | ENST00000634258.3 | |||
SZT2 | NM_015284.4 | c.8745+8G>A | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SZT2 | ENST00000634258.3 | c.8916+8G>A | splice_region_variant, intron_variant | 5 | NM_001365999.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000690 AC: 105AN: 152234Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000159 AC: 40AN: 251096Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135734
GnomAD4 exome AF: 0.0000766 AC: 112AN: 1461214Hom.: 0 Cov.: 30 AF XY: 0.0000592 AC XY: 43AN XY: 726916
GnomAD4 genome ? AF: 0.000689 AC: 105AN: 152352Hom.: 1 Cov.: 33 AF XY: 0.000658 AC XY: 49AN XY: 74512
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 03, 2015 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 26, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at