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

Variant summary

Our verdict is Benign. The variant received -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

Publications

16 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198268.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
HIPK1	NM_198268.3	MANE Select	c.*196C>T	3_prime_UTR	Exon 16 of 16	NP_938009.1
HIPK1	NM_001369806.1		c.*196C>T	3_prime_UTR	Exon 16 of 16	NP_001356735.1
HIPK1	NM_001369807.1		c.*196C>T	3_prime_UTR	Exon 16 of 16	NP_001356736.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
HIPK1	ENST00000426820.7	TSL:2 MANE Select	c.*196C>T	3_prime_UTR	Exon 16 of 16	ENSP00000407442.3
HIPK1	ENST00000369558.5	TSL:1	c.*196C>T	3_prime_UTR	Exon 16 of 16	ENSP00000358571.1
HIPK1	ENST00000340480.8	TSL:1	c.*196C>T	3_prime_UTR	Exon 15 of 15	ENSP00000340956.4

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

African (AFR)

AF:

0.230

AC:

1945

AN:

8448

American (AMR)

AF:

0.189

AC:

1562

AN:

8260

Ashkenazi Jewish (ASJ)

AF:

0.191

AC:

1988

AN:

10408

East Asian (EAS)

AF:

0.237

AC:

5578

AN:

23560

South Asian (SAS)

AF:

0.115

AC:

1185

AN:

10348

European-Finnish (FIN)

AF:

0.331

AC:

7595

AN:

22948

Middle Eastern (MID)

AF:

0.154

AC:

241

AN:

1562

European-Non Finnish (NFE)

AF:

0.241

AC:

52451

AN:

217526

Other (OTH)

AF:

0.224

AC:

4436

AN:

19784

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

2800

5599

8399

11198

13998

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

606

1212

1818

2424

3030

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.240

AC:

36440

AN:

152022

Hom.:

4487

Cov.:

AF XY:

0.242

AC XY:

17998

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.225

AC:

9326

AN:

41462

American (AMR)

AF:

0.216

AC:

3299

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.204

AC:

708

AN:

3466

East Asian (EAS)

AF:

0.244

AC:

1261

AN:

5174

South Asian (SAS)

AF:

0.132

AC:

635

AN:

4812

European-Finnish (FIN)

AF:

0.347

AC:

3663

AN:

10544

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.247

AC:

16794

AN:

67960

Other (OTH)

AF:

0.224

AC:

473

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1445

2890

4334

5779

7224

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

380

760

1140

1520

1900

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.235

Hom.:

5499

Bravo

AF:

0.231

Asia WGS

AF:

0.208

AC:

725

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

0.64

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over