rs1263014900

Variant names:

• chr12-123311112-T-A
• rs1263014900
• NM_001167856.3:c.3238A>T

Your query was ambiguous. Multiple possible variants found:

• chr12-123311112-T-A
• chr12-123311112-T-C

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001167856.3(SBNO1):​c.3238A>T​(p.Ile1080Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I1080V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SBNO1 NM_001167856.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.64
• Publications: 1 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: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.26729125).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SBNO1	NM_001167856.3	c.3238A>T	p.Ile1080Leu	missense_variant	Exon 25 of 32	ENST00000602398.3	NP_001161328.1
SBNO1	NM_018183.5	c.3235A>T	p.Ile1079Leu	missense_variant	Exon 25 of 32		NP_060653.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SBNO1	ENST00000602398.3	c.3238A>T	p.Ile1080Leu	missense_variant	Exon 25 of 32	5	NM_001167856.3	ENSP00000473665.1
SBNO1	ENST00000420886.6	c.3238A>T	p.Ile1080Leu	missense_variant	Exon 24 of 31	1		ENSP00000387361.2
SBNO1	ENST00000267176.8	c.3235A>T	p.Ile1079Leu	missense_variant	Exon 25 of 32	5		ENSP00000267176.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000398 AC: 1 AN: 251236 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000880

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.33
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Uncertain	24
DANN	Benign	0.97
DEOGEN2	Benign	0.025	T;.;T
Eigen	Benign	-0.24
Eigen_PC	Benign	-0.030
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.87	D;D;.
M_CAP	Benign	0.0083	T
MetaRNN	Benign	0.27	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	-0.69	N;.;N
PhyloP100		3.6
PrimateAI	Uncertain	0.67	T
PROVEAN	Benign	-1.1	N;N;.
REVEL	Benign	0.15
Sift	Benign	0.46	T;T;.
Sift4G	Benign	0.47	T;T;T
Polyphen		0.23	B;B;B
Vest4		0.59
MutPred		0.44		Loss of sheet (P = 0.0357);.;Loss of sheet (P = 0.0357);
MVP		0.23
MPC		0.76
ClinPred		0.34	T
GERP RS		4.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.18
gMVP		0.58
Mutation Taster		=86/14	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1263014900; hg19: chr12-123795659;