ENST00000722334.1:n.206+7817T>C

Variant names:

• chr1-113920427-A-G
• rs11811771
• ENST00000722334.1:n.206+7817T>C

Variant summary

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

The ENST00000722334.1(HIPK1-AS1):​n.206+7817T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,874 control chromosomes in the GnomAD database, including 14,494 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 0.43 (14494 hom., cov: 31)
• Consequence: HIPK1-AS1 ENST00000722334.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 16 publications found

Genes affected

HIPK1-AS1 (HGNC:50576): (HIPK1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722334.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HIPK1-AS1	ENST00000722334.1		n.206+7817T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65837 AN: 151756 Hom.: 14491 Cov.: 31

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.434 AC: 65874 AN: 151874 Hom.: 14494 Cov.: 31 AF XY: 0.431 AC XY: 31964 AN XY: 74206

African (AFR) AF: 0.446 AC: 18469 AN: 41402

American (AMR) AF: 0.448 AC: 6829 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1780 AN: 3472

East Asian (EAS) AF: 0.592 AC: 3055 AN: 5158

South Asian (SAS) AF: 0.433 AC: 2082 AN: 4812

European-Finnish (FIN) AF: 0.358 AC: 3772 AN: 10522

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28452 AN: 67948

Other (OTH) AF: 0.437 AC: 922 AN: 2112

Alfa AF: 0.409 Hom.: 7476

Bravo AF: 0.443

Asia WGS AF: 0.477 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.4
DANN	Benign	0.81
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs11811771; hg19: chr1-114463049;