ENST00000427953.5:n.272G>C

Variant names:

• chr1-113928961-C-G
• rs3811019
• ENST00000427953.5:n.272G>C

Variant summary

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

The ENST00000427953.5(HIPK1-AS1):​n.272G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0748 in 203,232 control chromosomes in the GnomAD database, including 1,063 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 0.072 (721 hom., cov: 33)
  • Exomes 𝑓: 0.082 (342 hom.)
• Consequence: HIPK1-AS1 ENST00000427953.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.742
• Publications: 12 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=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000427953.5. 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
	HIPK1-AS1	NR_110725.1		n.298G>C		non_coding_transcript_exon	Exon 1 of 5
	HIPK1-AS1	NR_110726.1		n.164+401G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HIPK1-AS1	ENST00000427953.5	TSL:1	n.272G>C		non_coding_transcript_exon	Exon 1 of 2
	HIPK1-AS1	ENST00000450706.1	TSL:1	n.298G>C		non_coding_transcript_exon	Exon 1 of 5
	HIPK1-AS1	ENST00000670954.2		n.535G>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0724 AC: 11018 AN: 152122 Hom.: 724 Cov.: 33

Gnomad AFR AF: 0.0163

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.0567

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0689

Gnomad OTH AF: 0.0826

GnomAD4 exome AF: 0.0822 AC: 4192 AN: 50992 Hom.: 342 Cov.: 0 AF XY: 0.0774 AC XY: 2111 AN XY: 27272

African (AFR) AF: 0.0111 AC: 23 AN: 2072

American (AMR) AF: 0.139 AC: 462 AN: 3334

Ashkenazi Jewish (ASJ) AF: 0.0477 AC: 57 AN: 1196

East Asian (EAS) AF: 0.364 AC: 971 AN: 2664

South Asian (SAS) AF: 0.0449 AC: 401 AN: 8934

European-Finnish (FIN) AF: 0.0979 AC: 190 AN: 1940

Middle Eastern (MID) AF: 0.0781 AC: 15 AN: 192

European-Non Finnish (NFE) AF: 0.0660 AC: 1855 AN: 28106

Other (OTH) AF: 0.0854 AC: 218 AN: 2554

GnomAD4 genome AF: 0.0724 AC: 11018 AN: 152240 Hom.: 721 Cov.: 33 AF XY: 0.0752 AC XY: 5597 AN XY: 74430

African (AFR) AF: 0.0163 AC: 676 AN: 41548

American (AMR) AF: 0.122 AC: 1872 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0576 AC: 200 AN: 3472

East Asian (EAS) AF: 0.358 AC: 1856 AN: 5182

South Asian (SAS) AF: 0.0572 AC: 276 AN: 4828

European-Finnish (FIN) AF: 0.112 AC: 1182 AN: 10596

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0689 AC: 4685 AN: 67996

Other (OTH) AF: 0.0851 AC: 180 AN: 2116

Alfa AF: 0.0651 Hom.: 49

Bravo AF: 0.0755

Asia WGS AF: 0.200 AC: 693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	15
DANN	Benign	0.74
PhyloP100		0.74
PromoterAI		0.078	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3811019; hg19: chr1-114471583;