rs2649999

Variant names:

• chr12-120942741-T-C
• rs2649999
• ENST00000619441.2:n.296-799A>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.296-799A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 151,756 control chromosomes in the GnomAD database, including 37,982 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 (37982 hom., cov: 29)
• Consequence: HNF1A-AS1 ENST00000619441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 10 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 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.296-799A>G		intron_variant	Intron 1 of 1	3
HNF1A-AS1	ENST00000760046.1	n.411-799A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105802 AN: 151638 Hom.: 37927 Cov.: 29

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.698 AC: 105914 AN: 151756 Hom.: 37982 Cov.: 29 AF XY: 0.686 AC XY: 50861 AN XY: 74158

African (AFR) AF: 0.877 AC: 36347 AN: 41424

American (AMR) AF: 0.647 AC: 9822 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1840 AN: 3464

East Asian (EAS) AF: 0.527 AC: 2719 AN: 5158

South Asian (SAS) AF: 0.582 AC: 2797 AN: 4802

European-Finnish (FIN) AF: 0.546 AC: 5716 AN: 10478

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.657 AC: 44660 AN: 67948

Other (OTH) AF: 0.672 AC: 1412 AN: 2100

Alfa AF: 0.680 Hom.: 4503

Bravo AF: 0.715

Asia WGS AF: 0.555 AC: 1935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.92
DANN	Benign	0.32
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2649999; hg19: chr12-121380544;