dbSNP rs3746162: SBNO2:c.2077+111G>A (chr19-1114120-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.112

Publications

15 publications found

Variant links:

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]

SBNO2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SBNO2	NM_014963.3 link	c.2077+111G>A		intron_variant	Intron 18 of 31	ENST00000361757.8	NP_055778.2	Q9Y2G9-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SBNO2	ENST00000361757.8 link	c.2077+111G>A	intron_variant	Intron 18 of 31	1	NM_014963.3	ENSP00000354733.2	Q9Y2G9-1
SBNO2	ENST00000587024.5 link	c.2047+111G>A	intron_variant	Intron 18 of 31	2		ENSP00000468520.1	K7ES28
SBNO2	ENST00000438103.6 link	c.1906+111G>A	intron_variant	Intron 15 of 28	2		ENSP00000400762.1	Q9Y2G9-3

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27491

AN:

152028

Hom.:

2812

Cov.:

show subpopulations

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

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

7328

14656

21985

29313

36641

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4688

9376

14064

18752

23440

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.181

AC:

27511

AN:

152146

Hom.:

2815

Cov.:

AF XY:

0.183

AC XY:

13573

AN XY:

74372

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.219

AC:

14917

AN:

67970

Other (OTH)

AF:

0.180

AC:

379

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1168

2336

3504

4672

5840

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

304

608

912

1216

1520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

6.7

(source)

DANN

Benign

0.62

PhyloP100

0.11

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over