rs1464798

Variant names:

• chr7-139647254-G-A
• rs1464798
• NM_022740.5:c.1104-15529C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-139647254-G-A
• chr7-139647254-G-C
• chr7-139647254-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022740.5(HIPK2):​c.1104-15529C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 151,780 control chromosomes in the GnomAD database, including 17,220 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 0.46 (17220 hom., cov: 30)
• Consequence: HIPK2 NM_022740.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HIPK2	NM_022740.5	c.1104-15529C>T		intron_variant	Intron 2 of 14	ENST00000406875.8	NP_073577.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HIPK2	ENST00000406875.8	c.1104-15529C>T		intron_variant	Intron 2 of 14	1	NM_022740.5	ENSP00000385571.3
HIPK2	ENST00000428878.6	c.1104-15529C>T		intron_variant	Intron 2 of 14	1		ENSP00000413724.2
HIPK2	ENST00000342645.7	c.1083-15529C>T		intron_variant	Intron 1 of 10	5		ENSP00000343108.7

Frequencies

GnomAD3 genomes AF: 0.462 AC: 69999 AN: 151662 Hom.: 17190 Cov.: 30

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.0860

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.462 AC: 70077 AN: 151780 Hom.: 17220 Cov.: 30 AF XY: 0.455 AC XY: 33749 AN XY: 74156

African (AFR) AF: 0.593 AC: 24537 AN: 41344

American (AMR) AF: 0.311 AC: 4754 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1456 AN: 3470

East Asian (EAS) AF: 0.0854 AC: 441 AN: 5164

South Asian (SAS) AF: 0.388 AC: 1865 AN: 4808

European-Finnish (FIN) AF: 0.452 AC: 4760 AN: 10526

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30659 AN: 67900

Other (OTH) AF: 0.438 AC: 920 AN: 2102

Alfa AF: 0.448 Hom.: 36466

Bravo AF: 0.453

Asia WGS AF: 0.265 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.45
PhyloP100		-0.23

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

Other links and lift over

dbSNP: rs1464798; hg19: chr7-139332000;