chr7-139653387-T-C

Position:

• chr7-139653387-T-C

Variant summary

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

The NM_022740.5(HIPK2):​c.1104-21662A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 150,696 control chromosomes in the GnomAD database, including 29,443 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 0.62 (29443 hom., cov: 26)
• Consequence: HIPK2 NM_022740.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HIPK2	NM_022740.5	c.1104-21662A>G		intron_variant		ENST00000406875.8	NP_073577.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HIPK2	ENST00000406875.8	c.1104-21662A>G		intron_variant		1	NM_022740.5	ENSP00000385571.3
HIPK2	ENST00000428878.6	c.1104-21662A>G		intron_variant		1		ENSP00000413724.2
HIPK2	ENST00000342645.7	c.1083-21662A>G		intron_variant		5		ENSP00000343108.7

Frequencies

GnomAD3 genomes AF: 0.623 AC: 93790 AN: 150576 Hom.: 29440 Cov.: 26

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.609

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.623 AC: 93813 AN: 150696 Hom.: 29443 Cov.: 26 AF XY: 0.614 AC XY: 45180 AN XY: 73536

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.647

Alfa AF: 0.655 Hom.: 36803

Bravo AF: 0.625

Asia WGS AF: 0.472 AC: 1644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.61

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: rs11761839; hg19: chr7-139338133;