rs1920792

Positions:

• chr12-120966781-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000619441.1(HNF1A-AS1):​n.128+13863A>G variant causes a intron, non coding transcript 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 ENST00000619441.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HNF1A-AS1	ENST00000619441.1	n.128+13863A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.410

Alfa AF: 0.424 Hom.: 2689

Bravo AF: 0.419

Asia WGS AF: 0.429 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1920792; hg19: chr12-121404584;