rs148055910
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001172509.2(SATB2):c.1071C>T(p.Ser357=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000905 in 1,612,388 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 (★★).
Frequency
Genomes: 𝑓 0.00033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000065 ( 0 hom. )
Consequence
SATB2
NM_001172509.2 synonymous
NM_001172509.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.813
Genes affected
SATB2 (HGNC:21637): (SATB homeobox 2) This gene encodes a DNA binding protein that specifically binds nuclear matrix attachment regions. The encoded protein is involved in transcription regulation and chromatin remodeling. Defects in this gene are associated with isolated cleft palate and cognitive disability. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
?
Variant 2-199348803-G-A is Benign according to our data. Variant chr2-199348803-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 537279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.813 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000335 (51/152282) while in subpopulation AFR AF= 0.000962 (40/41564). AF 95% confidence interval is 0.000726. There are 0 homozygotes in gnomad4. There are 30 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 51 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SATB2 | NM_001172509.2 | c.1071C>T | p.Ser357= | synonymous_variant | 7/11 | ENST00000417098.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SATB2 | ENST00000417098.6 | c.1071C>T | p.Ser357= | synonymous_variant | 7/11 | 2 | NM_001172509.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000335 AC: 51AN: 152164Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000998 AC: 25AN: 250436Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135278
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GnomAD4 exome AF: 0.0000651 AC: 95AN: 1460106Hom.: 0 Cov.: 31 AF XY: 0.0000579 AC XY: 42AN XY: 726004
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GnomAD4 genome ? AF: 0.000335 AC: 51AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.000403 AC XY: 30AN XY: 74458
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 04, 2019 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 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. - |
Chromosome 2q32-q33 deletion syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 19, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at