rs140116634
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001172509.2(SATB2):āc.333G>Cā(p.Ala111=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000367 in 1,613,834 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 (ā ā ). Synonymous variant affecting the same amino acid position (i.e. A111A) 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.333G>C | p.Ala111= | synonymous_variant | 3/11 | ENST00000417098.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SATB2 | ENST00000417098.6 | c.333G>C | p.Ala111= | synonymous_variant | 3/11 | 2 | NM_001172509.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000147 AC: 37AN: 250910Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135612
GnomAD4 exome AF: 0.000381 AC: 557AN: 1461556Hom.: 0 Cov.: 31 AF XY: 0.000369 AC XY: 268AN XY: 727058
GnomAD4 genome AF: 0.000230 AC: 35AN: 152278Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74450
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2020 | - - |
Chromosome 2q32-q33 deletion syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at