rs181831231
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001365999.1(SZT2):c.7975-10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00145 in 1,612,080 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001365999.1 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SZT2 | ENST00000634258.3 | c.7975-10C>T | intron_variant | Intron 57 of 71 | 5 | NM_001365999.1 | ENSP00000489255.1 | |||
SZT2 | ENST00000562955.2 | c.7804-10C>T | intron_variant | Intron 56 of 70 | 5 | ENSP00000457168.1 | ||||
SZT2 | ENST00000648058.1 | n.4429-10C>T | intron_variant | Intron 25 of 39 | ||||||
SZT2 | ENST00000649403.1 | n.2725-10C>T | intron_variant | Intron 22 of 36 |
Frequencies
GnomAD3 genomes AF: 0.00146 AC: 222AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00399 AC: 996AN: 249586Hom.: 8 AF XY: 0.00402 AC XY: 542AN XY: 134796
GnomAD4 exome AF: 0.00145 AC: 2112AN: 1459788Hom.: 34 Cov.: 36 AF XY: 0.00168 AC XY: 1223AN XY: 725914
GnomAD4 genome AF: 0.00145 AC: 221AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.00154 AC XY: 115AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
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Developmental and epileptic encephalopathy, 18 Benign:1
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SZT2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at