chr12-120967323-C-A

Position:

• chr12-120967323-C-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+13321G>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 0.701 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 ENST00000619441.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297

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 (AFR) allele frequency at 95% confidence interval = 0.881 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+13321G>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.673

Alfa AF: 0.644 Hom.: 49270

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2251468; hg19: chr12-121405126;