rs747745210
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001172509.2(SATB2):c.1173+6A>G variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0001 in 1,567,242 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 0.00012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000098 ( 0 hom. )
Consequence
SATB2
NM_001172509.2 splice_donor_region, intron
NM_001172509.2 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.0001921
2
Clinical Significance
Conservation
PhyloP100: 0.184
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 2-199348695-T-C is Benign according to our data. Variant chr2-199348695-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 469540.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000118 (18/152346) while in subpopulation NFE AF= 0.000235 (16/68030). AF 95% confidence interval is 0.000147. There are 0 homozygotes in gnomad4. There are 8 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High AC in GnomAd at 18 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SATB2 | NM_001172509.2 | c.1173+6A>G | splice_donor_region_variant, intron_variant | ENST00000417098.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SATB2 | ENST00000417098.6 | c.1173+6A>G | splice_donor_region_variant, intron_variant | 2 | NM_001172509.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152228Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000696 AC: 15AN: 215482Hom.: 0 AF XY: 0.0000874 AC XY: 10AN XY: 114358
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GnomAD4 exome AF: 0.0000982 AC: 139AN: 1414896Hom.: 0 Cov.: 28 AF XY: 0.000111 AC XY: 78AN XY: 700156
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GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152346Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74496
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 19, 2021 | - - |
Chromosome 2q32-q33 deletion syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at