rs139486476
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_001365999.1(SZT2):c.7573G>A(p.Val2525Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00119 in 1,614,176 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V2525G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001365999.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SZT2 | NM_001365999.1 | c.7573G>A | p.Val2525Ile | missense_variant | 54/72 | ENST00000634258.3 | |
SZT2 | NM_015284.4 | c.7402G>A | p.Val2468Ile | missense_variant | 53/71 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SZT2 | ENST00000634258.3 | c.7573G>A | p.Val2525Ile | missense_variant | 54/72 | 5 | NM_001365999.1 | P1 | |
SZT2 | ENST00000562955.2 | c.7402G>A | p.Val2468Ile | missense_variant | 53/71 | 5 | |||
SZT2 | ENST00000648058.1 | n.4027G>A | non_coding_transcript_exon_variant | 22/40 | |||||
SZT2 | ENST00000649403.1 | n.2323G>A | non_coding_transcript_exon_variant | 19/37 |
Frequencies
GnomAD3 genomes ? AF: 0.00652 AC: 992AN: 152172Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00173 AC: 434AN: 251412Hom.: 5 AF XY: 0.00132 AC XY: 179AN XY: 135866
GnomAD4 exome AF: 0.000634 AC: 927AN: 1461886Hom.: 15 Cov.: 52 AF XY: 0.000550 AC XY: 400AN XY: 727248
GnomAD4 genome ? AF: 0.00652 AC: 993AN: 152290Hom.: 9 Cov.: 32 AF XY: 0.00654 AC XY: 487AN XY: 74466
ClinVar
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 08, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Sep 14, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 31, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Developmental and epileptic encephalopathy, 18 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 23, 2018 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at