rs1555717920

Variant names:

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

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

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. 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

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SBNO2	NM_014963.3	c.3177_3189dupGCTGACGGGCCCC	p.Tyr1064AlafsTer6	frameshift_variant	Exon 28 of 32	ENST00000361757.8	NP_055778.2
SBNO2	NM_001100122.2	c.3006_3018dupGCTGACGGGCCCC	p.Tyr1007AlafsTer6	frameshift_variant	Exon 25 of 29		NP_001093592.1
SBNO2	XM_011527804.4	c.3177_3189dupGCTGACGGGCCCC	p.Tyr1064AlafsTer6	frameshift_variant	Exon 28 of 32		XP_011526106.1
SBNO2	XM_047438466.1	c.1980_1992dupGCTGACGGGCCCC	p.Tyr665AlafsTer6	frameshift_variant	Exon 25 of 29		XP_047294422.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SBNO2	ENST00000361757.8	c.3177_3189dupGCTGACGGGCCCC	p.Tyr1064AlafsTer6	frameshift_variant	Exon 28 of 32	1	NM_014963.3	ENSP00000354733.2

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

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555717920; hg19: chr19-1109531;