chr1-113923488-C-A

Variant names:

• chr1-113923488-C-A
• rs11102703
• ENST00000722334.1:n.206+4756G>T

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+4756G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,788 control chromosomes in the GnomAD database, including 7,993 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 0.32 (7993 hom., cov: 31)
• Consequence: HIPK1-AS1 ENST00000722334.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419
• Publications: 18 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 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.206+4756G>T		intron	N/A
	HIPK1-AS1	ENST00000722335.1		n.189-840G>T		intron	N/A
	HIPK1-AS1	ENST00000722336.1		n.206-840G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48244 AN: 151670 Hom.: 7983 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.318 AC: 48290 AN: 151788 Hom.: 7993 Cov.: 31 AF XY: 0.318 AC XY: 23601 AN XY: 74166

African (AFR) AF: 0.413 AC: 17071 AN: 41352

American (AMR) AF: 0.268 AC: 4095 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 875 AN: 3468

East Asian (EAS) AF: 0.253 AC: 1307 AN: 5168

South Asian (SAS) AF: 0.177 AC: 854 AN: 4818

European-Finnish (FIN) AF: 0.363 AC: 3806 AN: 10496

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.285 AC: 19366 AN: 67926

Other (OTH) AF: 0.297 AC: 627 AN: 2108

Alfa AF: 0.285 Hom.: 10576

Bravo AF: 0.316

Asia WGS AF: 0.254 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.61
DANN	Benign	0.28
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs11102703; hg19: chr1-114466110; COSMIC: COSV70179810;