5-136061329-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000358.3(TGFBI):c.1907-171T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 626,616 control chromosomes in the GnomAD database, including 92,961 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 0.59 ( 28180 hom., cov: 32)
Exomes 𝑓: 0.52 ( 64781 hom. )
Consequence
TGFBI
NM_000358.3 intron
NM_000358.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.23
Genes affected
TGFBI (HGNC:11771): (transforming growth factor beta induced) This gene encodes an RGD-containing protein that binds to type I, II and IV collagens. The RGD motif is found in many extracellular matrix proteins modulating cell adhesion and serves as a ligand recognition sequence for several integrins. This protein plays a role in cell-collagen interactions and may be involved in endochondrial bone formation in cartilage. The protein is induced by transforming growth factor-beta and acts to inhibit cell adhesion. Mutations in this gene are associated with multiple types of corneal dystrophy. [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=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TGFBI | NM_000358.3 | c.1907-171T>C | intron_variant | Intron 14 of 16 | ENST00000442011.7 | NP_000349.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.590 AC: 89692AN: 151892Hom.: 28135 Cov.: 32
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GnomAD4 exome AF: 0.517 AC: 245407AN: 474606Hom.: 64781 Cov.: 5 AF XY: 0.513 AC XY: 129232AN XY: 251728
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GnomAD4 genome AF: 0.591 AC: 89802AN: 152010Hom.: 28180 Cov.: 32 AF XY: 0.586 AC XY: 43548AN XY: 74292
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at