rs11210834
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005424.5(TIE1):c.3345+51A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 1,523,580 control chromosomes in the GnomAD database, including 48,187 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 0.24 ( 4524 hom., cov: 32)
Exomes 𝑓: 0.25 ( 43663 hom. )
Consequence
TIE1
NM_005424.5 intron
NM_005424.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.380
Genes affected
TIE1 (HGNC:11809): (tyrosine kinase with immunoglobulin like and EGF like domains 1) This gene encodes a member of the tyrosine protein kinase family. The encoded protein plays a critical role in angiogenesis and blood vessel stability by inhibiting angiopoietin 1 signaling through the endothelial receptor tyrosine kinase Tie2. Ectodomain cleavage of the encoded protein relieves inhibition of Tie2 and is mediated by multiple factors including vascular endothelial growth factor. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TIE1 | NM_005424.5 | c.3345+51A>G | intron_variant | ENST00000372476.8 | |||
TIE1 | NM_001253357.2 | c.3210+51A>G | intron_variant | ||||
TIE1 | XM_005271163.3 | c.3216+51A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TIE1 | ENST00000372476.8 | c.3345+51A>G | intron_variant | 1 | NM_005424.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.239 AC: 36289AN: 151892Hom.: 4519 Cov.: 32
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GnomAD3 exomes AF: 0.269 AC: 41232AN: 153006Hom.: 5929 AF XY: 0.272 AC XY: 21887AN XY: 80480
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GnomAD4 exome AF: 0.250 AC: 342227AN: 1371570Hom.: 43663 Cov.: 26 AF XY: 0.251 AC XY: 169982AN XY: 677320
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GnomAD4 genome ? AF: 0.239 AC: 36313AN: 152010Hom.: 4524 Cov.: 32 AF XY: 0.242 AC XY: 18008AN XY: 74314
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at