rs10500127
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001164665.2(KIAA1549):c.187+27403G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00991 in 152,188 control chromosomes in the GnomAD database, including 16 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 0.0099 ( 16 hom., cov: 33)
Consequence
KIAA1549
NM_001164665.2 intron
NM_001164665.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0420
Genes affected
KIAA1549 (HGNC:22219): (KIAA1549) The protein encoded by this gene belongs to the UPF0606 family. This gene has been found to be fused to the BRAF oncogene in many cases of pilocytic astrocytoma. The fusion results from 2Mb tandem duplications at 7q34. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BS2
?
High Homozygotes in GnomAd4 at 16 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA1549 | NM_001164665.2 | c.187+27403G>T | intron_variant | ENST00000422774.2 | |||
KIAA1549 | NM_020910.3 | c.187+27403G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA1549 | ENST00000422774.2 | c.187+27403G>T | intron_variant | 1 | NM_001164665.2 | A2 | |||
KIAA1549 | ENST00000440172.5 | c.187+27403G>T | intron_variant | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00992 AC: 1508AN: 152068Hom.: 16 Cov.: 33
GnomAD3 genomes
?
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1508
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00991 AC: 1508AN: 152188Hom.: 16 Cov.: 33 AF XY: 0.00888 AC XY: 661AN XY: 74418
GnomAD4 genome
?
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1508
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152188
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33
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661
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74418
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8
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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