dbSNP rs10108: HIPK1:c.*196C>T (chr1-113973708-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.636

Variant links:

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]

HIPK1 links:

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ACMG classification

Classification made for transcript

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 rank	MANE	Protein	UniProt
HIPK1	NM_198268.3 link	c.*196C>T		3_prime_UTR_variant	Exon 16 of 16	ENST00000426820.7	NP_938009.1	Q86Z02-1B4DZ33

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HIPK1	ENST00000426820.7 link	c.*196C>T		3_prime_UTR_variant	Exon 16 of 16	2	NM_198268.3	ENSP00000407442.3		Q86Z02-1

Frequencies

GnomAD3 genomes

AF:

0.240

AC:

36413

AN:

151904

Hom.:

4481

Cov.:

show subpopulations

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.:

AF XY:

0.236

AC XY:

38781

AN XY:

164144

show subpopulations

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.:

AF XY:

0.242

AC XY:

17998

AN XY:

74294

show subpopulations

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

DANN

Benign

0.79

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over