rs11485101

Positions:

• chr1-113959346-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_198268.3(HIPK1):​c.1981+1055A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,028 control chromosomes in the GnomAD database, including 1,908 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 0.12 (1908 hom., cov: 32)
• Consequence: HIPK1 NM_198268.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72

Genes affected

HIPK1 (HGNC:19006): (homeodomain interacting protein kinase 1) The protein encoded by this gene belongs to the Ser/Thr family of protein kinases and HIPK subfamily. It phosphorylates homeodomain transcription factors and may also function as a co-repressor for homeodomain transcription factors. Alternative splicing results in four transcript variants encoding four distinct isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HIPK1	NM_198268.3	c.1981+1055A>G		intron_variant		ENST00000426820.7	NP_938009.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HIPK1	ENST00000426820.7	c.1981+1055A>G		intron_variant		2	NM_198268.3	ENSP00000407442	P1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18778 AN: 151910 Hom.: 1906 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0764

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0459

Gnomad SAS AF: 0.0675

Gnomad FIN AF: 0.0509

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0593

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.124 AC: 18799 AN: 152028 Hom.: 1908 Cov.: 32 AF XY: 0.121 AC XY: 9028 AN XY: 74306

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.0763

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.0459

Gnomad4 SAS AF: 0.0673

Gnomad4 FIN AF: 0.0509

Gnomad4 NFE AF: 0.0593

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0743 Hom.: 897

Bravo AF: 0.132

Asia WGS AF: 0.0800 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	18
DANN	Benign	0.63

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

Publications

LitVar

Other links and lift over

dbSNP: rs11485101; hg19: chr1-114501968;