rs4759375

Variant names:

• chr12-123311691-C-T
• rs4759375
• NM_001167856.3:c.3221-562G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001167856.3(SBNO1):​c.3221-562G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.082 (625 hom., cov: 19)
• Consequence: SBNO1 NM_001167856.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 78 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SBNO1	NM_001167856.3	c.3221-562G>A		intron_variant	Intron 24 of 31	ENST00000602398.3	NP_001161328.1
SBNO1	NM_018183.5	c.3218-562G>A		intron_variant	Intron 24 of 31		NP_060653.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SBNO1	ENST00000602398.3	c.3221-562G>A		intron_variant	Intron 24 of 31	5	NM_001167856.3	ENSP00000473665.1
SBNO1	ENST00000420886.6	c.3221-562G>A		intron_variant	Intron 23 of 30	1		ENSP00000387361.2
SBNO1	ENST00000267176.8	c.3218-562G>A		intron_variant	Intron 24 of 31	5		ENSP00000267176.4

Frequencies

GnomAD3 genomes AF: 0.0815 AC: 9917 AN: 121748 Hom.: 620 Cov.: 19

Gnomad AFR AF: 0.0760

Gnomad AMI AF: 0.0918

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0587

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0875

Gnomad MID AF: 0.0532

Gnomad NFE AF: 0.0596

Gnomad OTH AF: 0.0938

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

GnomAD4 genome AF: 0.0816 AC: 9934 AN: 121768 Hom.: 625 Cov.: 19 AF XY: 0.0856 AC XY: 4954 AN XY: 57848

African (AFR) AF: 0.0762 AC: 2312 AN: 30354

American (AMR) AF: 0.107 AC: 1187 AN: 11106

Ashkenazi Jewish (ASJ) AF: 0.0587 AC: 191 AN: 3252

East Asian (EAS) AF: 0.310 AC: 1360 AN: 4386

South Asian (SAS) AF: 0.142 AC: 512 AN: 3600

European-Finnish (FIN) AF: 0.0875 AC: 536 AN: 6124

Middle Eastern (MID) AF: 0.0500 AC: 13 AN: 260

European-Non Finnish (NFE) AF: 0.0596 AC: 3592 AN: 60280

Other (OTH) AF: 0.0980 AC: 159 AN: 1622

Alfa AF: 0.102 Hom.: 938

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.78
PhyloP100		0.0
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: rs4759375; hg19: chr12-123796238;