1-113947067-T-C

Position:

• chr1-113947067-T-C

Variant summary

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

The NM_198268.3(HIPK1):​c.1076+5608T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,082 control chromosomes in the GnomAD database, including 7,538 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 0.31 (7538 hom., cov: 32)
• Consequence: HIPK1 NM_198268.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HIPK1	NM_198268.3	c.1076+5608T>C		intron_variant		ENST00000426820.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HIPK1	ENST00000426820.7	c.1076+5608T>C		intron_variant		2	NM_198268.3	P1

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46648 AN: 151964 Hom.: 7522 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.307 AC: 46711 AN: 152082 Hom.: 7538 Cov.: 32 AF XY: 0.307 AC XY: 22842 AN XY: 74350

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.287

Alfa AF: 0.268 Hom.: 3504

Bravo AF: 0.305

Asia WGS AF: 0.251 AC: 874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.60

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: rs1503832; hg19: chr1-114489689;