12-120953868-C-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000619441.2(HNF1A-AS1):​n.296-11926G>A 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 0.0000089 (0 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

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>A		intron	N/A
	HNF1A-AS1	ENST00000760046.1		n.411-11926G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00000888 AC: 1 AN: 112580 Hom.: 0 Cov.: 14

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000321

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000888 AC: 1 AN: 112654 Hom.: 0 Cov.: 14 AF XY: 0.0000194 AC XY: 1 AN XY: 51602

African (AFR) AF: 0.00 AC: 0 AN: 30648

American (AMR) AF: 0.00 AC: 0 AN: 8936

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2940

East Asian (EAS) AF: 0.00 AC: 0 AN: 3698

South Asian (SAS) AF: 0.00 AC: 0 AN: 3070

European-Finnish (FIN) AF: 0.000321 AC: 1 AN: 3120

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 160

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 57954

Other (OTH) AF: 0.00 AC: 0 AN: 1426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.96
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;