chr3-18349210-A-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2
The NM_002971.6(SATB1):āc.2252T>Cā(p.Val751Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,614,122 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_002971.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SATB1 | NM_002971.6 | c.2252T>C | p.Val751Ala | missense_variant | 11/11 | ENST00000338745.11 | NP_002962.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SATB1 | ENST00000338745.11 | c.2252T>C | p.Val751Ala | missense_variant | 11/11 | 1 | NM_002971.6 | ENSP00000341024 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251298Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135840
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.0000344 AC XY: 25AN XY: 727240
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152258Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74444
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at