rs878129

Variant names:

• chr1-113916573-C-T
• rs878129
• ENST00000722334.1:n.207-4386G>A

Variant summary

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

The ENST00000722334.1(HIPK1-AS1):​n.207-4386G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,128 control chromosomes in the GnomAD database, including 3,677 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 0.19 (3677 hom., cov: 31)
• Consequence: HIPK1-AS1 ENST00000722334.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615
• Publications: 26 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HIPK1-AS1	ENST00000722334.1		n.207-4386G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29588 AN: 152010 Hom.: 3676 Cov.: 31

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.195 AC: 29589 AN: 152128 Hom.: 3677 Cov.: 31 AF XY: 0.199 AC XY: 14774 AN XY: 74358

African (AFR) AF: 0.0448 AC: 1860 AN: 41536

American (AMR) AF: 0.201 AC: 3072 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 710 AN: 3472

East Asian (EAS) AF: 0.251 AC: 1303 AN: 5182

South Asian (SAS) AF: 0.156 AC: 753 AN: 4824

European-Finnish (FIN) AF: 0.358 AC: 3780 AN: 10548

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17462 AN: 67982

Other (OTH) AF: 0.186 AC: 392 AN: 2112

Alfa AF: 0.226 Hom.: 2608

Bravo AF: 0.178

Asia WGS AF: 0.205 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.72
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs878129; hg19: chr1-114459195;