rs2701175

Variant names:

• chr12-120953868-C-A
• rs2701175
• ENST00000619441.2:n.296-11926G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-120953868-C-A
• chr12-120953868-C-G
• chr12-120953868-C-T

Variant summary

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

The ENST00000619441.2(HNF1A-AS1):​n.296-11926G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.73 (29420 hom., cov: 14)
• Consequence: HNF1A-AS1 ENST00000619441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 9 publications found

Genes affected

HNF1A-AS1 (HGNC:26785): (HNF1A antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000619441.2. 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
	HNF1A-AS1	ENST00000619441.2	TSL:3	n.296-11926G>T		intron	N/A
	HNF1A-AS1	ENST00000760046.1		n.411-11926G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.727 AC: 81614 AN: 112292 Hom.: 29384 Cov.: 14

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.657

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.727 AC: 81688 AN: 112366 Hom.: 29420 Cov.: 14 AF XY: 0.726 AC XY: 37372 AN XY: 51478

African (AFR) AF: 0.891 AC: 27254 AN: 30604

American (AMR) AF: 0.711 AC: 6333 AN: 8908

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 1742 AN: 2936

East Asian (EAS) AF: 0.614 AC: 2263 AN: 3686

South Asian (SAS) AF: 0.628 AC: 1917 AN: 3054

European-Finnish (FIN) AF: 0.615 AC: 1912 AN: 3110

Middle Eastern (MID) AF: 0.650 AC: 104 AN: 160

European-Non Finnish (NFE) AF: 0.671 AC: 38801 AN: 57788

Other (OTH) AF: 0.683 AC: 972 AN: 1424

Alfa AF: 0.678 Hom.: 3989

Bravo AF: 0.717

Asia WGS AF: 0.557 AC: 1854 AN: 3324

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.52
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs2701175; hg19: chr12-121391671;