NM_001167856.3:c.3480T>A

Variant names:

• chr12-123309546-A-T
• NM_001167856.3:c.3480T>A
• SBNO1 p.Asp1160Glu

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001167856.3(SBNO1):​c.3480T>A​(p.Asp1160Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SBNO1 NM_001167856.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.564
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.059149027).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001167856.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SBNO1	NM_001167856.3	MANE Select	c.3480T>A	p.Asp1160Glu	missense	Exon 27 of 32	NP_001161328.1	A3KN83-1
	SBNO1	NM_018183.5		c.3477T>A	p.Asp1159Glu	missense	Exon 27 of 32	NP_060653.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SBNO1	ENST00000602398.3	TSL:5 MANE Select	c.3480T>A	p.Asp1160Glu	missense	Exon 27 of 32	ENSP00000473665.1	A3KN83-1
	SBNO1	ENST00000420886.6	TSL:1	c.3480T>A	p.Asp1160Glu	missense	Exon 26 of 31	ENSP00000387361.2	A3KN83-1
	SBNO1	ENST00000267176.8	TSL:5	c.3477T>A	p.Asp1159Glu	missense	Exon 27 of 32	ENSP00000267176.4	A3KN83-2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.084
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	12
DANN	Benign	0.77
DEOGEN2	Benign	0.0082	T
Eigen	Benign	-0.89
Eigen_PC	Benign	-0.70
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Uncertain	0.89	D
M_CAP	Benign	0.0090	T
MetaRNN	Benign	0.059	T
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	-0.55	N
PhyloP100		0.56
PrimateAI	Uncertain	0.72	T
PROVEAN	Benign	1.2	N
REVEL	Benign	0.14
Sift	Benign	0.81	T
Sift4G	Benign	0.81	T
Varity_R		0.026
gMVP		0.40
Mutation Taster		=91/9	polymorphism

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr12-123794093;