chr8-107958036-T-TCA

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]

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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 HGVSp Effect #exon/exons MANE UniProt
RSPO2NM_178565.5 linkuse as main transcriptc.616+43_616+44insTG intron_variant ENST00000276659.10
RSPO2NM_001282863.2 linkuse as main transcriptc.424+43_424+44insTG intron_variant
RSPO2NM_001317942.2 linkuse as main transcriptc.415+43_415+44insTG intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RSPO2ENST00000276659.10 linkuse as main transcriptc.616+43_616+44insTG intron_variant 1 NM_178565.5 P1Q6UXX9-1
ENST00000665144.1 linkuse as main transcriptn.326-1173_326-1172dup intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.490
AC:
74299
AN:
151684
Hom.:
21399
Cov.:
0
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.:
16
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.:
0
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 submitterclinical testingGenome-Nilou LabNov 07, 2021- -
Tetraamelia syndrome 2 Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabNov 07, 2021- -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMay 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.

Other links and lift over

dbSNP: rs3039298; hg19: chr8-108970264; API