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GeneBe

12-123320488-G-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP4BS2

The NM_001167856.3(SBNO1):c.2611C>G(p.Pro871Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000146 in 1,613,974 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00015 ( 0 hom. )

Consequence

SBNO1
NM_001167856.3 missense

Scores

3
4
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.90
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PP2
Missense variant where missense usually causes diseases, SBNO1
BP4
Computational evidence support a benign effect (MetaRNN=0.27305675).
BS2
High AC in GnomAd at 24 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SBNO1NM_001167856.3 linkuse as main transcriptc.2611C>G p.Pro871Ala missense_variant 19/32 ENST00000602398.3
SBNO1NM_018183.5 linkuse as main transcriptc.2608C>G p.Pro870Ala missense_variant 19/32

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SBNO1ENST00000602398.3 linkuse as main transcriptc.2611C>G p.Pro871Ala missense_variant 19/325 NM_001167856.3 P4A3KN83-1
SBNO1ENST00000420886.6 linkuse as main transcriptc.2611C>G p.Pro871Ala missense_variant 18/311 P4A3KN83-1
SBNO1ENST00000267176.8 linkuse as main transcriptc.2608C>G p.Pro870Ala missense_variant 19/325 A1A3KN83-2

Frequencies

GnomAD3 genomes
AF:
0.000158
AC:
24
AN:
152120
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000193
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000577
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000191
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000227
AC:
57
AN:
251392
Hom.:
0
AF XY:
0.000243
AC XY:
33
AN XY:
135876
show subpopulations
Gnomad AFR exome
AF:
0.000246
Gnomad AMR exome
AF:
0.000116
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000816
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000924
Gnomad NFE exome
AF:
0.000255
Gnomad OTH exome
AF:
0.000489
GnomAD4 exome
AF:
0.000145
AC:
212
AN:
1461854
Hom.:
0
Cov.:
32
AF XY:
0.000139
AC XY:
101
AN XY:
727228
show subpopulations
Gnomad4 AFR exome
AF:
0.000179
Gnomad4 AMR exome
AF:
0.0000894
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000202
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.0000749
Gnomad4 NFE exome
AF:
0.000162
Gnomad4 OTH exome
AF:
0.000132
GnomAD4 genome
AF:
0.000158
AC:
24
AN:
152120
Hom.:
0
Cov.:
32
AF XY:
0.000188
AC XY:
14
AN XY:
74312
show subpopulations
Gnomad4 AFR
AF:
0.000193
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000577
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000191
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000164
Hom.:
0
Bravo
AF:
0.000159
ESP6500AA
AF:
0.000454
AC:
2
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.000206
AC:
25
EpiCase
AF:
0.000273
EpiControl
AF:
0.000415

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 submitterclinical testingAmbry GeneticsSep 29, 2023The c.2611C>G (p.P871A) alteration is located in exon 18 (coding exon 18) of the SBNO1 gene. This alteration results from a C to G substitution at nucleotide position 2611, causing the proline (P) at amino acid position 871 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.33
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.17
Cadd
Uncertain
23
Dann
Uncertain
1.0
DEOGEN2
Benign
0.22
T;.;T
Eigen
Uncertain
0.42
Eigen_PC
Uncertain
0.56
FATHMM_MKL
Pathogenic
1.0
D
LIST_S2
Uncertain
0.95
D;D;.
M_CAP
Benign
0.012
T
MetaRNN
Benign
0.27
T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.9
L;.;L
MutationTaster
Benign
1.0
D;D
PrimateAI
Pathogenic
0.83
D
PROVEAN
Pathogenic
-6.0
D;D;.
REVEL
Benign
0.28
Sift
Benign
0.29
T;T;.
Sift4G
Benign
0.41
T;T;T
Polyphen
0.37
B;P;B
Vest4
0.70
MVP
0.26
MPC
0.72
ClinPred
0.10
T
GERP RS
5.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.34
gMVP
0.82

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs149772827; hg19: chr12-123805035; API