chr19-1109532-A-AGGGGCCCGTCAGC
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014963.3(SBNO2):c.3189_3190insGCTGACGGGCCCC(p.Tyr1064AlafsTer6) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
SBNO2
NM_014963.3 frameshift
NM_014963.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0180
Genes affected
SBNO2 (HGNC:29158): (strawberry notch homolog 2) Predicted to enable chromatin DNA binding activity and histone binding activity. Involved in several processes, including cellular response to interleukin-6; macrophage activation involved in immune response; and negative regulation of transcription, DNA-templated. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SBNO2 | NM_014963.3 | c.3189_3190insGCTGACGGGCCCC | p.Tyr1064AlafsTer6 | frameshift_variant | 28/32 | ENST00000361757.8 | |
SBNO2 | NM_001100122.2 | c.3018_3019insGCTGACGGGCCCC | p.Tyr1007AlafsTer6 | frameshift_variant | 25/29 | ||
SBNO2 | XM_011527804.4 | c.3189_3190insGCTGACGGGCCCC | p.Tyr1064AlafsTer6 | frameshift_variant | 28/32 | ||
SBNO2 | XM_047438466.1 | c.1992_1993insGCTGACGGGCCCC | p.Tyr665AlafsTer6 | frameshift_variant | 25/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SBNO2 | ENST00000361757.8 | c.3189_3190insGCTGACGGGCCCC | p.Tyr1064AlafsTer6 | frameshift_variant | 28/32 | 1 | NM_014963.3 | P2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 52
GnomAD4 exome
Cov.:
52
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 21, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at