rs2255531

chr12-120977112-G-A

Variant summary

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

The ENST00000619441.1(HNF1A-AS1):n.128+3532C>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 0.357 in 151,942 control chromosomes in the GnomAD database, including 9,911 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 0.36 (9911 hom., cov: 32)
• Consequence: HNF1A-AS1 ENST00000619441.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.456 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+3532C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54231 AN: 151824 Hom.: 9911 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.357 AC: 54253 AN: 151942 Hom.: 9911 Cov.: 32 AF XY: 0.365 AC XY: 27108 AN XY: 74262

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.375

Alfa AF: 0.360 Hom.: 2097

Bravo AF: 0.349

Asia WGS AF: 0.454 AC: 1575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.4
Dann	Benign	0.65
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2255531; hg19: chr12-121414915;