Variant chr12-123320714-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_001167856.3(SBNO1):c.2476C>T(p.Pro826Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0125 in 1,608,602 control chromosomes in the GnomAD database, including 151 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0090 ( 13 hom., cov: 32)

Exomes 𝑓: 0.013 ( 138 hom. )

Consequence

SBNO1
NM_001167856.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.06

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]

SBNO1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00358662).

BP6

Variant 12-123320714-G-A is Benign according to our data. Variant chr12-123320714-G-A is described in ClinVar as [Benign]. Clinvar id is 782334.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 1367 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SBNO1	NM_001167856.3 linkuse as main transcript	c.2476C>T	p.Pro826Ser	missense_variant	18/32	ENST00000602398.3	NP_001161328.1
SBNO1	NM_018183.5 linkuse as main transcript	c.2473C>T	p.Pro825Ser	missense_variant	18/32		NP_060653.3	A3KN83-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SBNO1	ENST00000602398.3 linkuse as main transcript	c.2476C>T	p.Pro826Ser	missense_variant	18/32	5	NM_001167856.3	ENSP00000473665.1	A3KN83-1
SBNO1	ENST00000420886.6 linkuse as main transcript	c.2476C>T	p.Pro826Ser	missense_variant	17/31	1		ENSP00000387361.2	A3KN83-1
SBNO1	ENST00000267176.8 linkuse as main transcript	c.2473C>T	p.Pro825Ser	missense_variant	18/32	5		ENSP00000267176.4	A3KN83-2

Frequencies

GnomAD3 genomes

AF:

0.00898

AC:

1366

AN:

152184

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00265

Gnomad AMI

AF:

0.00220

Gnomad AMR

AF:

0.00419

Gnomad ASJ

AF:

0.00663

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00642

Gnomad FIN

AF:

0.0102

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0149

Gnomad OTH

AF:

0.00573

GnomAD3 exomes

AF:

0.00911

AC:

2241

AN:

245886

Hom.:

AF XY:

0.00950

AC XY:

1263

AN XY:

132932

show subpopulations

Gnomad AFR exome

AF:

0.00198

Gnomad AMR exome

AF:

0.00459

Gnomad ASJ exome

AF:

0.00468

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00629

Gnomad FIN exome

AF:

0.00877

Gnomad NFE exome

AF:

0.0142

Gnomad OTH exome

AF:

0.00752

GnomAD4 exome

AF:

0.0129

AC:

18757

AN:

1456300

Hom.:

138

Cov.:

AF XY:

0.0127

AC XY:

9193

AN XY:

724390

show subpopulations

Gnomad4 AFR exome

AF:

0.00197

Gnomad4 AMR exome

AF:

0.00470

Gnomad4 ASJ exome

AF:

0.00440

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00664

Gnomad4 FIN exome

AF:

0.00946

Gnomad4 NFE exome

AF:

0.0149

Gnomad4 OTH exome

AF:

0.0119

GnomAD4 genome

AF:

0.00898

AC:

1367

AN:

152302

Hom.:

Cov.:

AF XY:

0.00832

AC XY:

620

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.00265

Gnomad4 AMR

AF:

0.00419

Gnomad4 ASJ

AF:

0.00663

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00663

Gnomad4 FIN

AF:

0.0102

Gnomad4 NFE

AF:

0.0149

Gnomad4 OTH

AF:

0.00567

Alfa

AF:

0.0119

Hom.:

Bravo

AF:

0.00825

TwinsUK

AF:

0.0159

AC:

ALSPAC

AF:

0.0119

AC:

ESP6500AA

AF:

0.00204

AC:

ESP6500EA

AF:

0.0121

AC:

104

ExAC

AF:

0.00905

AC:

1099

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.0118

EpiControl

AF:

0.0126

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.058

BayesDel_addAF

Benign

-0.69

BayesDel_noAF

Benign

-0.74

CADD

Benign

DANN

Benign

0.37

DEOGEN2

Benign

0.0097

T;.;T

Eigen

Benign

-0.68

Eigen_PC

Benign

-0.42

FATHMM_MKL

Uncertain

0.94

LIST_S2

Benign

0.76

T;T;.

MetaRNN

Benign

0.0036

T;T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

0.0

N;.;N

MutationTaster

Benign

0.99

N;N

PrimateAI

Benign

0.38

PROVEAN

Benign

-0.20

N;N;.

REVEL

Benign

0.085

Sift

Benign

0.59

T;T;.

Sift4G

Benign

0.76

T;T;T

Polyphen

0.0

B;B;B

Vest4

0.14

MVP

0.068

MPC

0.68

ClinPred

0.0023

GERP RS

2.9

Varity_R

0.021

gMVP

0.37

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over