rs3811019

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-113928961-C-A
• chr1-113928961-C-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000427953.5(HIPK1-AS1):​n.272G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HIPK1-AS1	NR_110725.1	n.298G>T		non_coding_transcript_exon_variant	Exon 1 of 5
HIPK1-AS1	NR_110726.1	n.164+401G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HIPK1-AS1	ENST00000427953.5	n.272G>T		non_coding_transcript_exon_variant	Exon 1 of 2	1
HIPK1-AS1	ENST00000450706.1	n.298G>T		non_coding_transcript_exon_variant	Exon 1 of 5	1
HIPK1-AS1	ENST00000670954.2	n.535G>T		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 51028 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 27292

African (AFR) AF: 0.00 AC: 0 AN: 2072

American (AMR) AF: 0.00 AC: 0 AN: 3340

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1196

East Asian (EAS) AF: 0.00 AC: 0 AN: 2674

South Asian (SAS) AF: 0.00 AC: 0 AN: 8936

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1942

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 192

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 28118

Other (OTH) AF: 0.00 AC: 0 AN: 2558

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	14
DANN	Benign	0.84
PhyloP100		0.74
PromoterAI		-0.020	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;