ENST00000619441.2:n.295+13321G>T

Variant names:

• chr12-120967323-C-A
• rs2251468
• ENST00000619441.2:n.295+13321G>T

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+13321G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 151,990 control chromosomes in the GnomAD database, including 38,488 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 0.70 (38488 hom., cov: 31)
• Consequence: HNF1A-AS1 ENST00000619441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• Publications: 54 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 (AFR) allele frequency at 95% confidence interval = 0.881 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+13321G>T		intron_variant	Intron 1 of 1	3
HNF1A-AS1	ENST00000646404.1	n.302-1408G>T		intron_variant	Intron 2 of 2
HNF1A-AS1	ENST00000647473.1	n.598+2975G>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106502 AN: 151870 Hom.: 38432 Cov.: 31

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.701 AC: 106617 AN: 151990 Hom.: 38488 Cov.: 31 AF XY: 0.691 AC XY: 51332 AN XY: 74252

African (AFR) AF: 0.889 AC: 36870 AN: 41490

American (AMR) AF: 0.650 AC: 9908 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1895 AN: 3468

East Asian (EAS) AF: 0.586 AC: 3026 AN: 5162

South Asian (SAS) AF: 0.586 AC: 2821 AN: 4818

European-Finnish (FIN) AF: 0.557 AC: 5868 AN: 10538

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44225 AN: 67958

Other (OTH) AF: 0.673 AC: 1421 AN: 2112

Alfa AF: 0.661 Hom.: 125508

Bravo AF: 0.718

Asia WGS AF: 0.582 AC: 2029 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	3.6
DANN	Benign	0.67
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs2251468; hg19: chr12-121405126;