12-123298029-C-G

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_001167856.3(SBNO1):​c.3988G>C​(p.Val1330Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1330M) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

SBNO1
NM_001167856.3 missense

Scores

2
3
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.89

Publications

2 publications found
Variant links:
Genes affected
SBNO1 (HGNC:22973): (strawberry notch homolog 1) Predicted to enable chromatin DNA binding activity and histone binding activity. Predicted to be involved in 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 was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.40690264).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SBNO1NM_001167856.3 linkc.3988G>C p.Val1330Leu missense_variant Exon 31 of 32 ENST00000602398.3 NP_001161328.1
SBNO1NM_018183.5 linkc.3985G>C p.Val1329Leu missense_variant Exon 31 of 32 NP_060653.3 A3KN83-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SBNO1ENST00000602398.3 linkc.3988G>C p.Val1330Leu missense_variant Exon 31 of 32 5 NM_001167856.3 ENSP00000473665.1 A3KN83-1
SBNO1ENST00000420886.6 linkc.3988G>C p.Val1330Leu missense_variant Exon 30 of 31 1 ENSP00000387361.2 A3KN83-1
SBNO1ENST00000267176.8 linkc.3985G>C p.Val1329Leu missense_variant Exon 31 of 32 5 ENSP00000267176.4 A3KN83-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.27
BayesDel_addAF
Benign
-0.024
T
BayesDel_noAF
Benign
-0.27
CADD
Uncertain
24
DANN
Benign
0.96
DEOGEN2
Benign
0.016
T;.;T
Eigen
Benign
0.044
Eigen_PC
Uncertain
0.24
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.95
D;D;.
M_CAP
Benign
0.030
D
MetaRNN
Benign
0.41
T;T;T
MetaSVM
Benign
-0.41
T
MutationAssessor
Benign
1.4
L;.;L
PhyloP100
5.9
PrimateAI
Pathogenic
0.89
D
PROVEAN
Benign
-0.44
N;N;.
REVEL
Uncertain
0.33
Sift
Benign
0.65
T;T;.
Sift4G
Benign
0.65
T;T;T
Polyphen
0.029
B;B;B
Vest4
0.69
MutPred
0.36
Loss of MoRF binding (P = 0.101);.;Loss of MoRF binding (P = 0.101);
MVP
0.19
MPC
0.69
ClinPred
0.81
D
GERP RS
5.6
Varity_R
0.063
gMVP
0.64
Mutation Taster
=75/25
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs114590549; hg19: chr12-123782576; API