chr11-33331063-A-T

Variant names:

• chr11-33331063-A-T
• rs266489
• NM_005734.5:c.1221+2430A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005734.5(HIPK3):​c.1221+2430A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: HIPK3 NM_005734.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005734.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HIPK3	NM_005734.5	MANE Select	c.1221+2430A>T		intron	N/A	NP_005725.3
	HIPK3	NM_001048200.3		c.1221+2430A>T		intron	N/A	NP_001041665.1
	HIPK3	NM_001278162.2		c.1221+2430A>T		intron	N/A	NP_001265091.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HIPK3	ENST00000303296.9	TSL:5 MANE Select	c.1221+2430A>T		intron	N/A	ENSP00000304226.4
	HIPK3	ENST00000379016.7	TSL:1	c.1221+2430A>T		intron	N/A	ENSP00000368301.3
	HIPK3	ENST00000525975.5	TSL:1	c.1221+2430A>T		intron	N/A	ENSP00000431710.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 5

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.93
DANN	Benign	0.22
PhyloP100		-1.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs266489; hg19: chr11-33352609;