12-123338164-G-A

Variant names:

• chr12-123338164-G-A
• rs7980687
• NM_001167856.3:c.652-1673C>T

Variant summary

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

The NM_001167856.3(SBNO1):​c.652-1673C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,128 control chromosomes in the GnomAD database, including 3,800 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 0.22 (3800 hom., cov: 33)
• Consequence: SBNO1 NM_001167856.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 58 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SBNO1	NM_001167856.3	c.652-1673C>T		intron_variant	Intron 5 of 31	ENST00000602398.3	NP_001161328.1
SBNO1	NM_018183.5	c.649-1673C>T		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.652-1673C>T		intron_variant	Intron 5 of 31	5	NM_001167856.3	ENSP00000473665.1
SBNO1	ENST00000420886.6	c.652-1673C>T		intron_variant	Intron 4 of 30	1		ENSP00000387361.2
SBNO1	ENST00000267176.8	c.649-1673C>T		intron_variant	Intron 5 of 31	5		ENSP00000267176.4

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32812 AN: 152010 Hom.: 3786 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.00423

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.216 AC: 32850 AN: 152128 Hom.: 3800 Cov.: 33 AF XY: 0.217 AC XY: 16114 AN XY: 74370

African (AFR) AF: 0.261 AC: 10842 AN: 41486

American (AMR) AF: 0.202 AC: 3084 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 895 AN: 3468

East Asian (EAS) AF: 0.00424 AC: 22 AN: 5192

South Asian (SAS) AF: 0.219 AC: 1056 AN: 4822

European-Finnish (FIN) AF: 0.225 AC: 2375 AN: 10572

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.204 AC: 13892 AN: 67994

Other (OTH) AF: 0.211 AC: 445 AN: 2110

Alfa AF: 0.208 Hom.: 9603

Bravo AF: 0.215

Asia WGS AF: 0.114 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.52
PhyloP100		-0.10
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: rs7980687; hg19: chr12-123822711;