rs3746162

Variant names:

• chr19-1114120-C-T
• rs3746162
• NM_014963.3:c.2077+111G>A

Variant summary

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

The NM_014963.3(SBNO2):​c.2077+111G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 1,029,976 control chromosomes in the GnomAD database, including 23,295 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 0.18 (2815 hom., cov: 33)
  • Exomes 𝑓: 0.21 (20480 hom.)
• Consequence: SBNO2 NM_014963.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 15 publications found

Genes affected

SBNO2 (HGNC:29158): (strawberry notch homolog 2) Predicted to enable chromatin DNA binding activity and histone binding activity. Involved in several processes, including cellular response to interleukin-6; macrophage activation involved in immune response; and negative 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 (NFE) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014963.3. 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
	SBNO2	NM_014963.3	MANE Select	c.2077+111G>A		intron	N/A	NP_055778.2	Q9Y2G9-1
	SBNO2	NM_001100122.2		c.1906+111G>A		intron	N/A	NP_001093592.1	Q9Y2G9-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SBNO2	ENST00000361757.8	TSL:1 MANE Select	c.2077+111G>A		intron	N/A	ENSP00000354733.2	Q9Y2G9-1
	SBNO2	ENST00000954690.1		c.2092+111G>A		intron	N/A	ENSP00000624749.1
	SBNO2	ENST00000935177.1		c.2077+111G>A		intron	N/A	ENSP00000605236.1

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27491 AN: 152028 Hom.: 2812 Cov.: 33

Gnomad AFR AF: 0.0884

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.176

GnomAD4 exome AF: 0.211 AC: 184975 AN: 877830 Hom.: 20480 AF XY: 0.209 AC XY: 90743 AN XY: 434106

African (AFR) AF: 0.0846 AC: 1575 AN: 18622

American (AMR) AF: 0.190 AC: 2620 AN: 13808

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 2614 AN: 15452

East Asian (EAS) AF: 0.134 AC: 3778 AN: 28116

South Asian (SAS) AF: 0.157 AC: 7511 AN: 47840

European-Finnish (FIN) AF: 0.296 AC: 10283 AN: 34786

Middle Eastern (MID) AF: 0.159 AC: 609 AN: 3828

European-Non Finnish (NFE) AF: 0.219 AC: 147932 AN: 676432

Other (OTH) AF: 0.207 AC: 8053 AN: 38946

GnomAD4 genome AF: 0.181 AC: 27511 AN: 152146 Hom.: 2815 Cov.: 33 AF XY: 0.183 AC XY: 13573 AN XY: 74372

African (AFR) AF: 0.0882 AC: 3662 AN: 41514

American (AMR) AF: 0.194 AC: 2959 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3466

East Asian (EAS) AF: 0.121 AC: 624 AN: 5174

South Asian (SAS) AF: 0.174 AC: 842 AN: 4826

European-Finnish (FIN) AF: 0.294 AC: 3115 AN: 10604

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14917 AN: 67970

Other (OTH) AF: 0.180 AC: 379 AN: 2106

Alfa AF: 0.209 Hom.: 5628

Bravo AF: 0.171

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.62
PhyloP100		0.11
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: rs3746162; hg19: chr19-1114119; COSMIC: COSV107475974; COSMIC: COSV107475974;