rs7456421
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_022740.5(HIPK2):āc.1059C>Gā(p.Val353=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 1,613,590 control chromosomes in the GnomAD database, including 55,700 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: š 0.36 ( 13715 hom., cov: 32)
Exomes š: 0.22 ( 41985 hom. )
Consequence
HIPK2
NM_022740.5 synonymous
NM_022740.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.701
Genes affected
HIPK2 (HGNC:14402): (homeodomain interacting protein kinase 2) This gene encodes a conserved serine/threonine kinase that is a member of the homeodomain-interacting protein kinase family. The encoded protein interacts with homeodomain transcription factors and many other transcription factors such as p53, and can function as both a corepressor and a coactivator depending on the transcription factor and its subcellular localization. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP7
?
Synonymous conserved (PhyloP=0.701 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIPK2 | NM_022740.5 | c.1059C>G | p.Val353= | synonymous_variant | 2/15 | ENST00000406875.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIPK2 | ENST00000406875.8 | c.1059C>G | p.Val353= | synonymous_variant | 2/15 | 1 | NM_022740.5 | A2 | |
HIPK2 | ENST00000428878.6 | c.1059C>G | p.Val353= | synonymous_variant | 2/15 | 1 | P4 | ||
HIPK2 | ENST00000342645.7 | c.1038C>G | p.Val346= | synonymous_variant | 1/11 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.359 AC: 54532AN: 151904Hom.: 13664 Cov.: 32
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GnomAD3 exomes AF: 0.271 AC: 67517AN: 248870Hom.: 12649 AF XY: 0.247 AC XY: 33411AN XY: 135198
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GnomAD4 exome AF: 0.216 AC: 316266AN: 1461566Hom.: 41985 Cov.: 34 AF XY: 0.212 AC XY: 153924AN XY: 727066
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GnomAD4 genome ? AF: 0.359 AC: 54651AN: 152024Hom.: 13715 Cov.: 32 AF XY: 0.358 AC XY: 26595AN XY: 74316
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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
RBP_binding_hub_radar
RBP_regulation_power_radar
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