rs1920792

Variant names:

• chr12-120966781-T-C
• rs1920792
• ENST00000619441.2:n.295+13863A>G

Variant summary

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

The ENST00000619441.2(HNF1A-AS1):​n.295+13863A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,762 control chromosomes in the GnomAD database, including 14,327 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 0.43 (14327 hom., cov: 31)
• Consequence: HNF1A-AS1 ENST00000619441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• Publications: 16 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 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.295+13863A>G		intron	N/A
	HNF1A-AS1	ENST00000646404.1		n.302-866A>G		intron	N/A
	HNF1A-AS1	ENST00000647473.1		n.599-3437A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65392 AN: 151644 Hom.: 14309 Cov.: 31

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.431 AC: 65445 AN: 151762 Hom.: 14327 Cov.: 31 AF XY: 0.425 AC XY: 31492 AN XY: 74152

African (AFR) AF: 0.414 AC: 17128 AN: 41388

American (AMR) AF: 0.295 AC: 4486 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1329 AN: 3466

East Asian (EAS) AF: 0.535 AC: 2767 AN: 5168

South Asian (SAS) AF: 0.364 AC: 1752 AN: 4812

European-Finnish (FIN) AF: 0.444 AC: 4657 AN: 10482

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32072 AN: 67910

Other (OTH) AF: 0.410 AC: 865 AN: 2110

Alfa AF: 0.455 Hom.: 22262

Bravo AF: 0.419

Asia WGS AF: 0.429 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.42
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs1920792; hg19: chr12-121404584;