rs2302109

chr19-1110830-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_014963.3(SBNO2):c.2943C>T(p.Asn981=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 1,613,160 control chromosomes in the GnomAD database, including 220,398 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 0.57 (24629 hom., cov: 31)
  • Exomes 𝑓: 0.52 (195769 hom.)
• Consequence: SBNO2 NM_014963.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.767

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

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BP7: Synonymous conserved (PhyloP=0.767 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SBNO2	NM_014963.3	c.2943C>T	p.Asn981=	synonymous_variant	26/32	ENST00000361757.8
SBNO2	NM_001100122.2	c.2772C>T	p.Asn924=	synonymous_variant	23/29
SBNO2	XM_011527804.4	c.2943C>T	p.Asn981=	synonymous_variant	26/32
SBNO2	XM_047438466.1	c.1746C>T	p.Asn582=	synonymous_variant	23/29

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SBNO2	ENST00000361757.8	c.2943C>T	p.Asn981=	synonymous_variant	26/32	1	NM_014963.3	P2

Frequencies

GnomAD3 genomes AF: 0.567 AC: 85921 AN: 151654 Hom.: 24591 Cov.: 31

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.539

GnomAD3 exomes AF: 0.536 AC: 133491 AN: 249062 Hom.: 36329 AF XY: 0.529 AC XY: 71457 AN XY: 135138

Gnomad AFR exome AF: 0.665

Gnomad AMR exome AF: 0.598

Gnomad ASJ exome AF: 0.498

Gnomad EAS exome AF: 0.473

Gnomad SAS exome AF: 0.523

Gnomad FIN exome AF: 0.600

Gnomad NFE exome AF: 0.505

Gnomad OTH exome AF: 0.505

GnomAD4 exome AF: 0.515 AC: 753322 AN: 1461388 Hom.: 195769 Cov.: 55 AF XY: 0.515 AC XY: 374177 AN XY: 727008

Gnomad4 AFR exome AF: 0.662

Gnomad4 AMR exome AF: 0.595

Gnomad4 ASJ exome AF: 0.498

Gnomad4 EAS exome AF: 0.529

Gnomad4 SAS exome AF: 0.515

Gnomad4 FIN exome AF: 0.597

Gnomad4 NFE exome AF: 0.505

Gnomad4 OTH exome AF: 0.510

GnomAD4 genome AF: 0.567 AC: 86015 AN: 151772 Hom.: 24629 Cov.: 31 AF XY: 0.571 AC XY: 42338 AN XY: 74154

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.543

Alfa AF: 0.517 Hom.: 38186

Bravo AF: 0.567

Asia WGS AF: 0.542 AC: 1886 AN: 3478

EpiCase AF: 0.497

EpiControl AF: 0.494

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
Cadd	Benign	1.3
Dann	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2302109; hg19: chr19-1110829; COSMIC: COSV62321060; COSMIC: COSV62321060;