rs266489
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_005734.5(HIPK3):c.1221+2430A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 151,834 control chromosomes in the GnomAD database, including 56 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 0.014 ( 56 hom., cov: 32)
Consequence
HIPK3
NM_005734.5 intron
NM_005734.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.28
Genes affected
HIPK3 (HGNC:4915): (homeodomain interacting protein kinase 3) Enables protein serine/threonine kinase activity. Involved in mRNA transcription; negative regulation of apoptotic process; and protein phosphorylation. Located in cytosol; nuclear body; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0141 (2146/151834) while in subpopulation AFR AF= 0.0487 (2017/41386). AF 95% confidence interval is 0.047. There are 56 homozygotes in gnomad4. There are 1042 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2134 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIPK3 | NM_005734.5 | c.1221+2430A>G | intron_variant | ENST00000303296.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIPK3 | ENST00000303296.9 | c.1221+2430A>G | intron_variant | 5 | NM_005734.5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0141 AC: 2134AN: 151716Hom.: 56 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0141 AC: 2146AN: 151834Hom.: 56 Cov.: 32 AF XY: 0.0140 AC XY: 1042AN XY: 74240
GnomAD4 genome
?
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2146
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1042
AN XY:
74240
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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