chr19-1108802-G-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_014963.3(SBNO2):c.3593C>G(p.Thr1198Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Consequence
SBNO2
NM_014963.3 missense
NM_014963.3 missense
Scores
4
11
3
Clinical Significance
Conservation
PhyloP100: 7.82
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 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.855
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SBNO2 | NM_014963.3 | c.3593C>G | p.Thr1198Ser | missense_variant | 31/32 | ENST00000361757.8 | |
SBNO2 | NM_001100122.2 | c.3422C>G | p.Thr1141Ser | missense_variant | 28/29 | ||
SBNO2 | XM_011527804.4 | c.3593C>G | p.Thr1198Ser | missense_variant | 31/32 | ||
SBNO2 | XM_047438466.1 | c.2396C>G | p.Thr799Ser | missense_variant | 28/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SBNO2 | ENST00000361757.8 | c.3593C>G | p.Thr1198Ser | missense_variant | 31/32 | 1 | NM_014963.3 | P2 | |
SBNO2 | ENST00000587024.5 | c.3563C>G | p.Thr1188Ser | missense_variant | 31/32 | 2 | A2 | ||
SBNO2 | ENST00000438103.6 | c.3422C>G | p.Thr1141Ser | missense_variant | 28/29 | 2 | A2 | ||
SBNO2 | ENST00000587673.5 | n.1046C>G | non_coding_transcript_exon_variant | 6/7 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 36
GnomAD4 exome
Cov.:
36
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2021 | The c.3593C>G (p.T1198S) alteration is located in exon 31 (coding exon 30) of the SBNO2 gene. This alteration results from a C to G substitution at nucleotide position 3593, causing the threonine (T) at amino acid position 1198 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;.;.
MutationTaster
Benign
N;N;N
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;D;.
REVEL
Uncertain
Sift
Uncertain
D;D;.
Sift4G
Uncertain
D;T;T
Polyphen
D;D;.
Vest4
MutPred
Gain of disorder (P = 0.0367);.;.;
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.