chr8-107958036-T-TCA
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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
NM_178565.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.05
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 |
---|---|---|---|---|---|---|---|
RSPO2 | NM_178565.5 | c.616+43_616+44insTG | intron_variant | ENST00000276659.10 | |||
RSPO2 | NM_001282863.2 | c.424+43_424+44insTG | intron_variant | ||||
RSPO2 | NM_001317942.2 | c.415+43_415+44insTG | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RSPO2 | ENST00000276659.10 | c.616+43_616+44insTG | intron_variant | 1 | NM_178565.5 | P1 | |||
ENST00000665144.1 | n.326-1173_326-1172dup | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.490 AC: 74299AN: 151684Hom.: 21399 Cov.: 0
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GnomAD3 exomes AF: 0.591 AC: 109724AN: 185756Hom.: 33992 AF XY: 0.600 AC XY: 60730AN XY: 101294
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GnomAD4 exome AF: 0.611 AC: 714573AN: 1168766Hom.: 223415 Cov.: 16 AF XY: 0.612 AC XY: 354158AN XY: 578342
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GnomAD4 genome AF: 0.490 AC: 74308AN: 151802Hom.: 21395 Cov.: 0 AF XY: 0.492 AC XY: 36459AN XY: 74164
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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
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at