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.

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.296-799A>G		intron	N/A
	HNF1A-AS1	ENST00000760046.1		n.411-799A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2649999;

hg19: chr12-121380544;