rs4807569

Variant names:

• chr19-1123379-A-C
• rs4807569
• NM_014963.3:c.628+155T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 35 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014963.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SBNO2	NM_014963.3	MANE Select	c.628+155T>G		intron	N/A	NP_055778.2
	SBNO2	NM_001100122.2		c.457+155T>G		intron	N/A	NP_001093592.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SBNO2	ENST00000361757.8	TSL:1 MANE Select	c.628+155T>G		intron	N/A	ENSP00000354733.2
	SBNO2	ENST00000592222.5	TSL:1	n.481+155T>G		intron	N/A
	SBNO2	ENST00000587024.5	TSL:2	c.628+155T>G		intron	N/A	ENSP00000468520.1

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

African (AFR) AF: 0.307 AC: 12709 AN: 41426

American (AMR) AF: 0.332 AC: 5071 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 699 AN: 3470

East Asian (EAS) AF: 0.128 AC: 664 AN: 5172

South Asian (SAS) AF: 0.220 AC: 1062 AN: 4822

European-Finnish (FIN) AF: 0.261 AC: 2758 AN: 10574

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.215 AC: 14585 AN: 67944

Other (OTH) AF: 0.255 AC: 538 AN: 2106

Alfa AF: 0.236 Hom.: 9062

Bravo AF: 0.259

Asia WGS AF: 0.192 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.52
PhyloP100		-2.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4807569; hg19: chr19-1123378; COSMIC: COSV107476012; COSMIC: COSV107476012;