dbSNP rs3811019: HIPK1-AS1:n.272G>T (chr1-113928961-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.742

Publications

12 publications found

Variant links:

Genes affected

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

HIPK1-AS1 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000427953.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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).

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>T		non_coding_transcript_exon	Exon 1 of 5
	HIPK1-AS1	NR_110726.1		n.164+401G>T		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

51028

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

27292

African (AFR)

AF:

0.00

AC:

AN:

2072

American (AMR)

AF:

0.00

AC:

AN:

3340

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1196

East Asian (EAS)

AF:

0.00

AC:

AN:

2674

South Asian (SAS)

AF:

0.00

AC:

AN:

8936

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1942

Middle Eastern (MID)

AF:

0.00

AC:

AN:

192

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

28118

Other (OTH)

AF:

0.00

AC:

AN:

2558

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

(source)

DANN

Benign

0.84

PhyloP100

0.74

PromoterAI

-0.020

Neutral

(source)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over