6-169229815-G-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003247.5(THBS2):c.2152-136C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 641,872 control chromosomes in the GnomAD database, including 118,137 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 0.65 ( 33210 hom., cov: 32)
Exomes 𝑓: 0.58 ( 84927 hom. )
Consequence
THBS2
NM_003247.5 intron
NM_003247.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.19
Genes affected
THBS2 (HGNC:11786): (thrombospondin 2) The protein encoded by this gene belongs to the thrombospondin family. It is a disulfide-linked homotrimeric glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. This protein has been shown to function as a potent inhibitor of tumor growth and angiogenesis. Studies of the mouse counterpart suggest that this protein may modulate the cell surface properties of mesenchymal cells and be involved in cell adhesion and migration. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.04).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THBS2 | NM_003247.5 | c.2152-136C>G | intron_variant | ENST00000617924.6 | |||
THBS2-AS1 | NR_134621.1 | n.682-9410G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THBS2 | ENST00000617924.6 | c.2152-136C>G | intron_variant | 1 | NM_003247.5 | P4 | |||
THBS2-AS1 | ENST00000660724.1 | n.640-9410G>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.650 AC: 98795AN: 151970Hom.: 33145 Cov.: 32
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GnomAD4 exome AF: 0.583 AC: 285575AN: 489784Hom.: 84927 AF XY: 0.583 AC XY: 149327AN XY: 256126
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GnomAD4 genome AF: 0.650 AC: 98922AN: 152088Hom.: 33210 Cov.: 32 AF XY: 0.648 AC XY: 48203AN XY: 74338
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at