chr12-120951159-A-C

Variant names:

• chr12-120951159-A-C
• rs2650000
• ENST00000619441.2:n.296-9217T>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.296-9217T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 152,024 control chromosomes in the GnomAD database, including 37,931 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 0.70 (37931 hom., cov: 32)
• Consequence: HNF1A-AS1 ENST00000619441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216
• Publications: 100 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HNF1A-AS1	ENST00000619441.2	n.296-9217T>G		intron_variant	Intron 1 of 1	3
HNF1A-AS1	ENST00000760046.1	n.411-9217T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105767 AN: 151906 Hom.: 37878 Cov.: 32

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.696 AC: 105878 AN: 152024 Hom.: 37931 Cov.: 32 AF XY: 0.686 AC XY: 50944 AN XY: 74300

African (AFR) AF: 0.878 AC: 36460 AN: 41506

American (AMR) AF: 0.646 AC: 9858 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1879 AN: 3472

East Asian (EAS) AF: 0.545 AC: 2812 AN: 5164

South Asian (SAS) AF: 0.588 AC: 2838 AN: 4826

European-Finnish (FIN) AF: 0.555 AC: 5849 AN: 10532

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44187 AN: 67962

Other (OTH) AF: 0.669 AC: 1411 AN: 2108

Alfa AF: 0.659 Hom.: 159168

Bravo AF: 0.712

Asia WGS AF: 0.566 AC: 1973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2650000; hg19: chr12-121388962;