rs11013962
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001098500.3(KIAA1217):c.-170-12969A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 152,076 control chromosomes in the GnomAD database, including 18,483 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 0.49 ( 18483 hom., cov: 33)
Consequence
KIAA1217
NM_001098500.3 intron
NM_001098500.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.656
Genes affected
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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=-0.7).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIAA1217 | NM_001098500.3 | c.-170-12969A>G | intron_variant | NP_001091970.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIAA1217 | ENST00000376462.5 | c.-170-12969A>G | intron_variant | 1 | ENSP00000365645.1 | |||||
KIAA1217 | ENST00000636305.1 | c.212-12969A>G | intron_variant | 5 | ENSP00000489926.1 |
Frequencies
GnomAD3 genomes AF: 0.488 AC: 74104AN: 151958Hom.: 18480 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.488 AC: 74145AN: 152076Hom.: 18483 Cov.: 33 AF XY: 0.488 AC XY: 36249AN XY: 74326
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at