rs2701175

chr12-120953868-C-Achr12-120953868-C-Gchr12-120953868-C-T

Variant summary

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

The ENST00000619441.1(HNF1A-AS1):n.129-11926G>T 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 0.727 in 112,366 control chromosomes in the GnomAD database, including 29,420 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 0.73 (29420 hom., cov: 14)
• Consequence: HNF1A-AS1 ENST00000619441.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 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.129-11926G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.727 AC: 81614 AN: 112292 Hom.: 29384 Cov.: 14

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.657

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.727 AC: 81688 AN: 112366 Hom.: 29420 Cov.: 14 AF XY: 0.726 AC XY: 37372 AN XY: 51478

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.683

Alfa AF: 0.678 Hom.: 3989

Bravo AF: 0.717

Asia WGS AF: 0.557 AC: 1854 AN: 3324

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.89
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2701175; hg19: chr12-121391671;