rs761385178
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4BP6BS1BS2
The NM_015559.3(SETBP1):āc.665G>Cā(p.Trp222Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,614,044 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. W222L) has been classified as Uncertain significance.
Frequency
Consequence
NM_015559.3 missense
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 |
---|---|---|---|---|---|---|---|
SETBP1 | NM_015559.3 | c.665G>C | p.Trp222Ser | missense_variant | 4/6 | ENST00000649279.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SETBP1 | ENST00000649279.2 | c.665G>C | p.Trp222Ser | missense_variant | 4/6 | NM_015559.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152206Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250962Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135664
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461838Hom.: 0 Cov.: 33 AF XY: 0.0000289 AC XY: 21AN XY: 727210
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152206Hom.: 1 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74338
ClinVar
Submissions by phenotype
Intellectual disability, autosomal dominant 29 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Mar 05, 2018 | - - |
Schinzel-Giedion syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Mar 05, 2018 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at