Variant rs2024092 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014963.3(SBNO2):c.442-10C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 1,607,266 control chromosomes in the GnomAD database, including 40,373 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 5098 hom., cov: 32)

Exomes 𝑓: 0.22 ( 35275 hom. )

Consequence

SBNO2
NM_014963.3 splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00001920

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00900

Variant links:

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]

SBNO2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SBNO2	NM_014963.3 linkuse as main transcript	c.442-10C>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000361757.8	NP_055778.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
SBNO2	ENST00000361757.8 linkuse as main transcript	c.442-10C>T	splice_polypyrimidine_tract_variant, intron_variant	1	NM_014963.3	ENSP00000354733	P2	Q9Y2G9-1
SBNO2	ENST00000592222.5 linkuse as main transcript	n.295-10C>T	splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant	1
SBNO2	ENST00000438103.6 linkuse as main transcript	c.271-10C>T	splice_polypyrimidine_tract_variant, intron_variant	2		ENSP00000400762	A2	Q9Y2G9-3
SBNO2	ENST00000587024.5 linkuse as main transcript	c.442-10C>T	splice_polypyrimidine_tract_variant, intron_variant	2		ENSP00000468520	A2

Frequencies

GnomAD3 genomes

AF:

0.253

AC:

38471

AN:

151964

Hom.:

5092

Cov.:

show subpopulations

Gnomad AFR

AF:

0.311

Gnomad AMI

AF:

0.188

Gnomad AMR

AF:

0.333

Gnomad ASJ

AF:

0.200

Gnomad EAS

AF:

0.129

Gnomad SAS

AF:

0.221

Gnomad FIN

AF:

0.259

Gnomad MID

AF:

0.248

Gnomad NFE

AF:

0.214

Gnomad OTH

AF:

0.259

GnomAD3 exomes

AF:

0.242

AC:

57574

AN:

238154

Hom.:

7423

AF XY:

0.235

AC XY:

30478

AN XY:

129784

show subpopulations

Gnomad AFR exome

AF:

0.304

Gnomad AMR exome

AF:

0.372

Gnomad ASJ exome

AF:

0.201

Gnomad EAS exome

AF:

0.131

Gnomad SAS exome

AF:

0.226

Gnomad FIN exome

AF:

0.248

Gnomad NFE exome

AF:

0.219

Gnomad OTH exome

AF:

0.224

GnomAD4 exome

AF:

0.215

AC:

313586

AN:

1455184

Hom.:

35275

Cov.:

AF XY:

0.215

AC XY:

155906

AN XY:

723490

show subpopulations

Gnomad4 AFR exome

AF:

0.309

Gnomad4 AMR exome

AF:

0.365

Gnomad4 ASJ exome

AF:

0.199

Gnomad4 EAS exome

AF:

0.162

Gnomad4 SAS exome

AF:

0.225

Gnomad4 FIN exome

AF:

0.241

Gnomad4 NFE exome

AF:

0.208

Gnomad4 OTH exome

AF:

0.207

GnomAD4 genome

AF:

0.253

AC:

38504

AN:

152082

Hom.:

5098

Cov.:

AF XY:

0.256

AC XY:

19033

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.311

Gnomad4 AMR

AF:

0.333

Gnomad4 ASJ

AF:

0.200

Gnomad4 EAS

AF:

0.129

Gnomad4 SAS

AF:

0.220

Gnomad4 FIN

AF:

0.259

Gnomad4 NFE

AF:

0.214

Gnomad4 OTH

AF:

0.257

Alfa

AF:

0.226

Hom.:

5901

Bravo

AF:

0.260

Asia WGS

AF:

0.193

AC:

673

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.5

DANN

Benign

0.60

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000019

dbscSNV1_RF

Benign

0.0020

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over