Variant rs2302109 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_014963.3(SBNO2):c.2943C>T(p.Asn981=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 1,613,160 control chromosomes in the GnomAD database, including 220,398 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 0.57 ( 24629 hom., cov: 31)

Exomes 𝑓: 0.52 ( 195769 hom. )

Consequence

SBNO2
NM_014963.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.767

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP7

Synonymous conserved (PhyloP=0.767 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SBNO2	NM_014963.3 linkuse as main transcript	c.2943C>T	p.Asn981=	synonymous_variant	26/32	ENST00000361757.8	NP_055778.2
SBNO2	NM_001100122.2 linkuse as main transcript	c.2772C>T	p.Asn924=	synonymous_variant	23/29		NP_001093592.1
SBNO2	XM_011527804.4 linkuse as main transcript	c.2943C>T	p.Asn981=	synonymous_variant	26/32		XP_011526106.1
SBNO2	XM_047438466.1 linkuse as main transcript	c.1746C>T	p.Asn582=	synonymous_variant	23/29		XP_047294422.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SBNO2	ENST00000361757.8 linkuse as main transcript	c.2943C>T	p.Asn981=	synonymous_variant	26/32	1	NM_014963.3	ENSP00000354733	P2	Q9Y2G9-1

Frequencies

GnomAD3 genomes

AF:

0.567

AC:

85921

AN:

151654

Hom.:

24591

Cov.:

show subpopulations

Gnomad AFR

AF:

0.663

Gnomad AMI

AF:

0.767

Gnomad AMR

AF:

0.591

Gnomad ASJ

AF:

0.497

Gnomad EAS

AF:

0.472

Gnomad SAS

AF:

0.528

Gnomad FIN

AF:

0.612

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.507

Gnomad OTH

AF:

0.539

GnomAD3 exomes

AF:

0.536

AC:

133491

AN:

249062

Hom.:

36329

AF XY:

0.529

AC XY:

71457

AN XY:

135138

show subpopulations

Gnomad AFR exome

AF:

0.665

Gnomad AMR exome

AF:

0.598

Gnomad ASJ exome

AF:

0.498

Gnomad EAS exome

AF:

0.473

Gnomad SAS exome

AF:

0.523

Gnomad FIN exome

AF:

0.600

Gnomad NFE exome

AF:

0.505

Gnomad OTH exome

AF:

0.505

GnomAD4 exome

AF:

0.515

AC:

753322

AN:

1461388

Hom.:

195769

Cov.:

AF XY:

0.515

AC XY:

374177

AN XY:

727008

show subpopulations

Gnomad4 AFR exome

AF:

0.662

Gnomad4 AMR exome

AF:

0.595

Gnomad4 ASJ exome

AF:

0.498

Gnomad4 EAS exome

AF:

0.529

Gnomad4 SAS exome

AF:

0.515

Gnomad4 FIN exome

AF:

0.597

Gnomad4 NFE exome

AF:

0.505

Gnomad4 OTH exome

AF:

0.510

GnomAD4 genome

AF:

0.567

AC:

86015

AN:

151772

Hom.:

24629

Cov.:

AF XY:

0.571

AC XY:

42338

AN XY:

74154

show subpopulations

Gnomad4 AFR

AF:

0.663

Gnomad4 AMR

AF:

0.591

Gnomad4 ASJ

AF:

0.497

Gnomad4 EAS

AF:

0.472

Gnomad4 SAS

AF:

0.528

Gnomad4 FIN

AF:

0.612

Gnomad4 NFE

AF:

0.507

Gnomad4 OTH

AF:

0.543

Alfa

AF:

0.517

Hom.:

38186

Bravo

AF:

0.567

Asia WGS

AF:

0.542

AC:

1886

AN:

3478

EpiCase

AF:

0.497

EpiControl

AF:

0.494

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

1.3

DANN

Benign

0.79

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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