rs4807569

Positions:

• chr19-1123379-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014963.3(SBNO2):​c.628+155T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 151,986 control chromosomes in the GnomAD database, including 5,074 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 (5074 hom., cov: 32)
• Consequence: SBNO2 NM_014963.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SBNO2	NM_014963.3	c.628+155T>G		intron_variant		ENST00000361757.8	NP_055778.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SBNO2	ENST00000361757.8	c.628+155T>G		intron_variant		1	NM_014963.3	ENSP00000354733.2
SBNO2	ENST00000592222.5	n.481+155T>G		intron_variant		1
SBNO2	ENST00000587024.5	c.628+155T>G		intron_variant		2		ENSP00000468520.1
SBNO2	ENST00000438103.6	c.457+155T>G		intron_variant		2		ENSP00000400762.1

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38291 AN: 151868 Hom.: 5067 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.258

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.252 AC: 38326 AN: 151986 Hom.: 5074 Cov.: 32 AF XY: 0.256 AC XY: 18984 AN XY: 74282

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.255

Alfa AF: 0.228 Hom.: 4697

Bravo AF: 0.259

Asia WGS AF: 0.192 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.52

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

Other links and lift over

dbSNP: rs4807569; hg19: chr19-1123378;