rs9297407

chr8-107997446-A-G

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The NM_178565.5(RSPO2):c.95-8202T>C variant causes a intron change. The variant allele was found at a frequency of 0.104 in 152,192 control chromosomes in the GnomAD database, including 2,089 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 0.10 (2089 hom., cov: 32)
• Consequence: RSPO2 NM_178565.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.35

Genes affected

RSPO2 (HGNC:28583): (R-spondin 2) This gene encodes a member of the R-spondin family of proteins. These proteins are secreted ligands of leucine-rich repeat containing G protein-coupled receptors that enhance Wnt signaling through the inhibition of ubiquitin E3 ligases. A chromosomal translocation including this locus that results in the formation of a gene fusion has been identified in multiple human cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.15).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSPO2	NM_178565.5	c.95-8202T>C		intron_variant		ENST00000276659.10
RSPO2	NM_001282863.2	c.95-36629T>C		intron_variant
RSPO2	NM_001317942.2	c.-107-8202T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSPO2	ENST00000276659.10	c.95-8202T>C		intron_variant		1	NM_178565.5	P1

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15792 AN: 152074 Hom.: 2087 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0442

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.0430

Gnomad FIN AF: 0.0247

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0800

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.104 AC: 15807 AN: 152192 Hom.: 2089 Cov.: 32 AF XY: 0.100 AC XY: 7481 AN XY: 74440

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.0440

Gnomad4 ASJ AF: 0.0415

Gnomad4 EAS AF: 0.0108

Gnomad4 SAS AF: 0.0428

Gnomad4 FIN AF: 0.0247

Gnomad4 NFE AF: 0.0191

Gnomad4 OTH AF: 0.0787

Alfa AF: 0.0545 Hom.: 174

Bravo AF: 0.114

Asia WGS AF: 0.0370 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.15
Cadd	Benign	20
Dann	Benign	0.84

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

LitVar

Other links and lift over

dbSNP: rs9297407; hg19: chr8-109009674;