rs11065374

chr12-120962402-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000619441.1(HNF1A-AS1):n.128+18242A>G variant causes a intron, non coding transcript 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 ENST00000619441.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

HNF1A-AS1 (HGNC:26785): (HNF1A antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HNF1A-AS1	ENST00000619441.1	n.128+18242A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.321

Alfa AF: 0.328 Hom.: 10137

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11065374; hg19: chr12-121400205;