1-113928961-C-G

Position:

• chr1-113928961-C-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HIPK1-AS1	NR_110726.1	n.164+401G>C		intron_variant, non_coding_transcript_variant
HIPK1-AS1	NR_110725.1	n.298G>C		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HIPK1-AS1	ENST00000670954.1	n.535G>C		non_coding_transcript_exon_variant	1/2

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

Gnomad4 AFR exome AF: 0.0111

Gnomad4 AMR exome AF: 0.139

Gnomad4 ASJ exome AF: 0.0477

Gnomad4 EAS exome AF: 0.364

Gnomad4 SAS exome AF: 0.0449

Gnomad4 FIN exome AF: 0.0979

Gnomad4 NFE exome AF: 0.0660

Gnomad4 OTH exome AF: 0.0854

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

Gnomad4 AFR AF: 0.0163

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0576

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.0572

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.0689

Gnomad4 OTH AF: 0.0851

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	15
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3811019; hg19: chr1-114471583;