rs11065374

Variant names:

• chr12-120962402-T-C
• rs11065374
• ENST00000619441.2:n.295+18242A>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.295+18242A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,886 control chromosomes in the GnomAD database, including 8,855 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 0.34 (8855 hom., cov: 32)
• Consequence: HNF1A-AS1 ENST00000619441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 13 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 (AFR) allele frequency at 95% confidence interval = 0.4 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.295+18242A>G		intron_variant	Intron 1 of 1	3
HNF1A-AS1	ENST00000760046.1	n.410+12083A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50899 AN: 151766 Hom.: 8840 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.335 AC: 50952 AN: 151886 Hom.: 8855 Cov.: 32 AF XY: 0.332 AC XY: 24680 AN XY: 74236

African (AFR) AF: 0.405 AC: 16762 AN: 41398

American (AMR) AF: 0.400 AC: 6110 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 930 AN: 3468

East Asian (EAS) AF: 0.144 AC: 744 AN: 5164

South Asian (SAS) AF: 0.319 AC: 1533 AN: 4800

European-Finnish (FIN) AF: 0.217 AC: 2301 AN: 10592

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21534 AN: 67896

Other (OTH) AF: 0.321 AC: 677 AN: 2108

Alfa AF: 0.328 Hom.: 12042

Bravo AF: 0.354

Asia WGS AF: 0.205 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.34
DANN	Benign	0.31
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11065374; hg19: chr12-121400205;