rs11830103

Variant names:

• chr12-123338999-A-G
• rs11830103
• NM_001167856.3:c.651+1989T>C

Variant summary

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

The NM_001167856.3(SBNO1):​c.651+1989T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 150,978 control chromosomes in the GnomAD database, including 6,650 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 0.27 (6650 hom., cov: 28)
• Consequence: SBNO1 NM_001167856.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

Genes affected

SBNO1 (HGNC:22973): (strawberry notch homolog 1) Predicted to enable chromatin DNA binding activity and histone binding activity. Predicted to be involved in 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SBNO1	NM_001167856.3	c.651+1989T>C		intron_variant	Intron 5 of 31	ENST00000602398.3	NP_001161328.1
SBNO1	NM_018183.5	c.648+1989T>C		intron_variant	Intron 5 of 31		NP_060653.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SBNO1	ENST00000602398.3	c.651+1989T>C		intron_variant	Intron 5 of 31	5	NM_001167856.3	ENSP00000473665.1
SBNO1	ENST00000420886.6	c.651+1989T>C		intron_variant	Intron 4 of 30	1		ENSP00000387361.2
SBNO1	ENST00000267176.8	c.648+1989T>C		intron_variant	Intron 5 of 31	5		ENSP00000267176.4

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40675 AN: 150860 Hom.: 6634 Cov.: 28

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.00429

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.270 AC: 40732 AN: 150978 Hom.: 6650 Cov.: 28 AF XY: 0.268 AC XY: 19710 AN XY: 73682

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.00430

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.249

Alfa AF: 0.238 Hom.: 1854

Bravo AF: 0.278

Asia WGS AF: 0.126 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.50

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: rs11830103; hg19: chr12-123823546;