rs10108

chr1-113973708-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198268.3(HIPK1):c.*196C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 474,866 control chromosomes in the GnomAD database, including 14,058 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 0.24 (4487 hom., cov: 32)
  • Exomes 𝑓: 0.24 (9571 hom.)
• Consequence: HIPK1 NM_198268.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.636

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HIPK1	NM_198268.3	c.*196C>T		3_prime_UTR_variant	16/16	ENST00000426820.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HIPK1	ENST00000426820.7	c.*196C>T		3_prime_UTR_variant	16/16	2	NM_198268.3	P1

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36413 AN: 151904 Hom.: 4481 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.224

GnomAD4 exome AF: 0.238 AC: 76981 AN: 322844 Hom.: 9571 Cov.: 5 AF XY: 0.236 AC XY: 38781 AN XY: 164144

Gnomad4 AFR exome AF: 0.230

Gnomad4 AMR exome AF: 0.189

Gnomad4 ASJ exome AF: 0.191

Gnomad4 EAS exome AF: 0.237

Gnomad4 SAS exome AF: 0.115

Gnomad4 FIN exome AF: 0.331

Gnomad4 NFE exome AF: 0.241

Gnomad4 OTH exome AF: 0.224

GnomAD4 genome AF: 0.240 AC: 36440 AN: 152022 Hom.: 4487 Cov.: 32 AF XY: 0.242 AC XY: 17998 AN XY: 74294

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.224

Alfa AF: 0.236 Hom.: 4249

Bravo AF: 0.231

Asia WGS AF: 0.208 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
Cadd	Benign	14
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10108; hg19: chr1-114516330; COSMIC: COSV61246860; COSMIC: COSV61246860;