rs368537092
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001172509.2(SATB2):c.1174-6A>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000348 in 1,610,562 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001172509.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SATB2 | NM_001172509.2 | c.1174-6A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000417098.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SATB2 | ENST00000417098.6 | c.1174-6A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | NM_001172509.2 | P1 | |||
ENST00000489557.2 | n.385T>A | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000722 AC: 18AN: 249466Hom.: 0 AF XY: 0.0000593 AC XY: 8AN XY: 134836
GnomAD4 exome AF: 0.0000350 AC: 51AN: 1458306Hom.: 0 Cov.: 28 AF XY: 0.0000345 AC XY: 25AN XY: 725674
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74446
ClinVar
Submissions by phenotype
Chromosome 2q32-q33 deletion syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at