rs143484322
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001172509.2(SATB2):c.2088C>T(p.Thr696=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00026 in 1,614,072 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T696T) has been classified as Likely benign.
Frequency
Consequence
NM_001172509.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SATB2 | NM_001172509.2 | c.2088C>T | p.Thr696= | synonymous_variant | 11/11 | ENST00000417098.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SATB2 | ENST00000417098.6 | c.2088C>T | p.Thr696= | synonymous_variant | 11/11 | 2 | NM_001172509.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000207 AC: 52AN: 251148Hom.: 0 AF XY: 0.000250 AC XY: 34AN XY: 135730
GnomAD4 exome AF: 0.000272 AC: 398AN: 1461868Hom.: 0 Cov.: 31 AF XY: 0.000293 AC XY: 213AN XY: 727238
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74410
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2017 | 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. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 24, 2021 | - - |
Chromosome 2q32-q33 deletion syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at