Variant 8-107958036-T-TCA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_178565.5(RSPO2):c.616+43_616+44insTG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.49 ( 21395 hom., cov: 0)

Exomes 𝑓: 0.61 ( 223415 hom. )

Consequence

RSPO2
NM_178565.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.05

Variant links:

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]

RSPO2 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 8-107958036-T-TCA is Benign according to our data. Variant chr8-107958036-T-TCA is described in ClinVar as [Benign]. Clinvar id is 1230819.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
RSPO2	NM_178565.5 linkuse as main transcript	c.616+43_616+44insTG	intron_variant	ENST00000276659.10
RSPO2	NM_001282863.2 linkuse as main transcript	c.424+43_424+44insTG	intron_variant
RSPO2	NM_001317942.2 linkuse as main transcript	c.415+43_415+44insTG	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSPO2	ENST00000276659.10 linkuse as main transcript	c.616+43_616+44insTG		intron_variant		1	NM_178565.5	P1	Q6UXX9-1
	ENST00000665144.1 linkuse as main transcript	n.326-1173_326-1172dup		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.490

AC:

74299

AN:

151684

Hom.:

21399

Cov.:

show subpopulations

Gnomad AFR

AF:

0.158

Gnomad AMI

AF:

0.659

Gnomad AMR

AF:

0.572

Gnomad ASJ

AF:

0.590

Gnomad EAS

AF:

0.693

Gnomad SAS

AF:

0.597

Gnomad FIN

AF:

0.593

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.625

Gnomad OTH

AF:

0.538

GnomAD3 exomes

AF:

0.591

AC:

109724

AN:

185756

Hom.:

33992

AF XY:

0.600

AC XY:

60730

AN XY:

101294

show subpopulations

Gnomad AFR exome

AF:

0.150

Gnomad AMR exome

AF:

0.620

Gnomad ASJ exome

AF:

0.599

Gnomad EAS exome

AF:

0.695

Gnomad SAS exome

AF:

0.606

Gnomad FIN exome

AF:

0.594

Gnomad NFE exome

AF:

0.626

Gnomad OTH exome

AF:

0.616

GnomAD4 exome

AF:

0.611

AC:

714573

AN:

1168766

Hom.:

223415

Cov.:

AF XY:

0.612

AC XY:

354158

AN XY:

578342

show subpopulations

Gnomad4 AFR exome

AF:

0.141

Gnomad4 AMR exome

AF:

0.607

Gnomad4 ASJ exome

AF:

0.586

Gnomad4 EAS exome

AF:

0.669

Gnomad4 SAS exome

AF:

0.607

Gnomad4 FIN exome

AF:

0.597

Gnomad4 NFE exome

AF:

0.625

Gnomad4 OTH exome

AF:

0.605

GnomAD4 genome

AF:

0.490

AC:

74308

AN:

151802

Hom.:

21395

Cov.:

AF XY:

0.492

AC XY:

36459

AN XY:

74164

show subpopulations

Gnomad4 AFR

AF:

0.157

Gnomad4 AMR

AF:

0.572

Gnomad4 ASJ

AF:

0.590

Gnomad4 EAS

AF:

0.692

Gnomad4 SAS

AF:

0.598

Gnomad4 FIN

AF:

0.593

Gnomad4 NFE

AF:

0.625

Gnomad4 OTH

AF:

0.537

Alfa

AF:

0.562

Hom.:

5414

Bravo

AF:

0.478

Asia WGS

AF:

0.589

AC:

2043

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Humerofemoral hypoplasia with radiotibial ray deficiency

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Nov 07, 2021

- -

Tetraamelia syndrome 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Nov 07, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over