NM_022740.5:c.*4893A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_022740.5(HIPK2):​c.*4893A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,336 control chromosomes in the GnomAD database, including 42,350 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 0.74 ( 42297 hom., cov: 32)
Exomes 𝑓: 0.69 ( 53 hom. )

Consequence

HIPK2
NM_022740.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.89

Publications

6 publications found
Variant links:
Genes affected
HIPK2 (HGNC:14402): (homeodomain interacting protein kinase 2) This gene encodes a conserved serine/threonine kinase that is a member of the homeodomain-interacting protein kinase family. The encoded protein interacts with homeodomain transcription factors and many other transcription factors such as p53, and can function as both a corepressor and a coactivator depending on the transcription factor and its subcellular localization. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

Genome browser will be placed here

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=-0.58).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HIPK2NM_022740.5 linkc.*4893A>G 3_prime_UTR_variant Exon 15 of 15 ENST00000406875.8 NP_073577.3 Q9H2X6-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HIPK2ENST00000406875.8 linkc.*4893A>G 3_prime_UTR_variant Exon 15 of 15 1 NM_022740.5 ENSP00000385571.3 Q9H2X6-1

Frequencies

GnomAD3 genomes
AF:
0.740
AC:
112474
AN:
151992
Hom.:
42229
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.836
Gnomad AMI
AF:
0.713
Gnomad AMR
AF:
0.785
Gnomad ASJ
AF:
0.667
Gnomad EAS
AF:
0.915
Gnomad SAS
AF:
0.808
Gnomad FIN
AF:
0.722
Gnomad MID
AF:
0.807
Gnomad NFE
AF:
0.659
Gnomad OTH
AF:
0.755
GnomAD4 exome
AF:
0.690
AC:
156
AN:
226
Hom.:
53
Cov.:
0
AF XY:
0.657
AC XY:
117
AN XY:
178
show subpopulations
African (AFR)
AF:
1.00
AC:
4
AN:
4
American (AMR)
AF:
1.00
AC:
2
AN:
2
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
0.750
AC:
3
AN:
4
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.789
AC:
30
AN:
38
Middle Eastern (MID)
AF:
1.00
AC:
2
AN:
2
European-Non Finnish (NFE)
AF:
0.646
AC:
102
AN:
158
Other (OTH)
AF:
0.722
AC:
13
AN:
18
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.519
Heterozygous variant carriers
0
2
4
6
8
10
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
2
4
6
8
10
<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:
0.740
AC:
112601
AN:
152110
Hom.:
42297
Cov.:
32
AF XY:
0.746
AC XY:
55468
AN XY:
74362
show subpopulations
African (AFR)
AF:
0.837
AC:
34715
AN:
41490
American (AMR)
AF:
0.786
AC:
12013
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.667
AC:
2313
AN:
3468
East Asian (EAS)
AF:
0.915
AC:
4732
AN:
5174
South Asian (SAS)
AF:
0.809
AC:
3899
AN:
4822
European-Finnish (FIN)
AF:
0.722
AC:
7621
AN:
10556
Middle Eastern (MID)
AF:
0.813
AC:
239
AN:
294
European-Non Finnish (NFE)
AF:
0.659
AC:
44818
AN:
67992
Other (OTH)
AF:
0.757
AC:
1602
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1477
2954
4432
5909
7386
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
842
1684
2526
3368
4210
<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:
0.698
Hom.:
66893
Bravo
AF:
0.750
Asia WGS
AF:
0.876
AC:
3046
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.58
CADD
Benign
9.8
DANN
Benign
0.80
PhyloP100
1.9

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

Other links and lift over

dbSNP: rs1638195; hg19: chr7-139252780; API