rs141108624
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015559.3(SETBP1):āc.3790T>Gā(p.Ser1264Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,614,120 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_015559.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SETBP1 | NM_015559.3 | c.3790T>G | p.Ser1264Ala | missense_variant | 4/6 | ENST00000649279.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SETBP1 | ENST00000649279.2 | c.3790T>G | p.Ser1264Ala | missense_variant | 4/6 | NM_015559.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000519 AC: 79AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000163 AC: 41AN: 250858Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135550
GnomAD4 exome AF: 0.0000588 AC: 86AN: 1461872Hom.: 0 Cov.: 65 AF XY: 0.0000399 AC XY: 29AN XY: 727240
GnomAD4 genome ? AF: 0.000525 AC: 80AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.000605 AC XY: 45AN XY: 74434
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 14, 2020 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 29, 2017 | - - |
SETBP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 15, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at