12-120965129-C-T

Variant names:

• chr12-120965129-C-T
• rs7305618
• ENST00000619441.2:n.295+15515G>A

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+15515G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,930 control chromosomes in the GnomAD database, including 6,799 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 0.28 (6799 hom., cov: 31)
• Consequence: HNF1A-AS1 ENST00000619441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 63 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 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+15515G>A		intron	N/A
	HNF1A-AS1	ENST00000647473.1		n.599-1785G>A		intron	N/A
	HNF1A-AS1	ENST00000760046.1		n.410+9356G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42948 AN: 151812 Hom.: 6777 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.283 AC: 43010 AN: 151930 Hom.: 6799 Cov.: 31 AF XY: 0.280 AC XY: 20752 AN XY: 74238

African (AFR) AF: 0.400 AC: 16560 AN: 41378

American (AMR) AF: 0.184 AC: 2808 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 879 AN: 3470

East Asian (EAS) AF: 0.533 AC: 2740 AN: 5144

South Asian (SAS) AF: 0.273 AC: 1318 AN: 4822

European-Finnish (FIN) AF: 0.207 AC: 2191 AN: 10560

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15739 AN: 67966

Other (OTH) AF: 0.269 AC: 569 AN: 2114

Alfa AF: 0.249 Hom.: 22486

Bravo AF: 0.288

Asia WGS AF: 0.392 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.60
PhyloP100		-0.067
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

Splicing

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

Other links and lift over

dbSNP: rs7305618; hg19: chr12-121402932;