rs2255531

Variant names:

• chr12-120977112-G-A
• rs2255531
• ENST00000433033.4:n.154-191C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000433033.4(HNF1A-AS1):​n.154-191C>T variant causes a intron 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 ENST00000433033.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363
• Publications: 19 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=-0.9).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HNF1A-AS1	ENST00000433033.4	n.154-191C>T		intron_variant	Intron 1 of 3	3
HNF1A-AS1	ENST00000535301.2	n.323-2514C>T		intron_variant	Intron 1 of 1	4
HNF1A-AS1	ENST00000537361.2	n.291+3532C>T		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.286 AC: 11839 AN: 41418

American (AMR) AF: 0.390 AC: 5945 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1670 AN: 3466

East Asian (EAS) AF: 0.411 AC: 2128 AN: 5180

South Asian (SAS) AF: 0.473 AC: 2279 AN: 4822

European-Finnish (FIN) AF: 0.418 AC: 4408 AN: 10548

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24545 AN: 67942

Other (OTH) AF: 0.375 AC: 789 AN: 2106

Alfa AF: 0.346 Hom.: 4052

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
PhyloP100		0.36
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

Other links and lift over

dbSNP: rs2255531; hg19: chr12-121414915;