NM_014963.3:c.3177_3189dupGCTGACGGGCCCC

Variant names:

• chr19-1109532-A-AGGGGCCCGTCAGC
• rs1555717920
• NM_014963.3:c.3177_3189dupGCTGACGGGCCCC

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_014963.3(SBNO2):​c.3177_3189dupGCTGACGGGCCCC​(p.Tyr1064AlafsTer6) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SBNO2 NM_014963.3 frameshift
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.0180
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

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.3177_3189dupGCTGACGGGCCCC	p.Tyr1064AlafsTer6	frameshift	Exon 28 of 32	NP_055778.2
	SBNO2	NM_001100122.2		c.3006_3018dupGCTGACGGGCCCC	p.Tyr1007AlafsTer6	frameshift	Exon 25 of 29	NP_001093592.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SBNO2	ENST00000361757.8	TSL:1 MANE Select	c.3177_3189dupGCTGACGGGCCCC	p.Tyr1064AlafsTer6	frameshift	Exon 28 of 32	ENSP00000354733.2
	SBNO2	ENST00000587024.5	TSL:2	c.3147_3159dupGCTGACGGGCCCC	p.Tyr1054AlafsTer6	frameshift	Exon 28 of 32	ENSP00000468520.1
	SBNO2	ENST00000438103.6	TSL:2	c.3006_3018dupGCTGACGGGCCCC	p.Tyr1007AlafsTer6	frameshift	Exon 25 of 29	ENSP00000400762.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 52

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Jun 21, 2018

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.018

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1555717920; hg19: chr19-1109531;