rs7953249

Variant names:

• chr12-120965921-G-A
• rs7953249
• ENST00000619441.2:n.295+14723C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-120965921-G-A
• chr12-120965921-G-C

Variant summary

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

The ENST00000646404.1(HNF1A-AS1):​n.302-6C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,036 control chromosomes in the GnomAD database, including 25,923 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 0.58 (25916 hom., cov: 32)
  • Exomes 𝑓: 0.47 (7 hom.)
• Consequence: HNF1A-AS1 ENST00000646404.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858
• Publications: 76 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646404.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HNF1A-AS1	ENST00000619441.2	TSL:3	n.295+14723C>T		intron	N/A
	HNF1A-AS1	ENST00000646404.1		n.302-6C>T		splice_region intron	N/A
	HNF1A-AS1	ENST00000647473.1		n.599-2577C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88282 AN: 151852 Hom.: 25882 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.562

GnomAD4 exome AF: 0.469 AC: 30 AN: 64 Hom.: 7 Cov.: 0 AF XY: 0.405 AC XY: 17 AN XY: 42

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.250 AC: 1 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.480 AC: 24 AN: 50

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.581 AC: 88371 AN: 151972 Hom.: 25916 Cov.: 32 AF XY: 0.572 AC XY: 42449 AN XY: 74270

African (AFR) AF: 0.656 AC: 27189 AN: 41454

American (AMR) AF: 0.557 AC: 8496 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1653 AN: 3468

East Asian (EAS) AF: 0.538 AC: 2779 AN: 5166

South Asian (SAS) AF: 0.442 AC: 2130 AN: 4814

European-Finnish (FIN) AF: 0.486 AC: 5142 AN: 10572

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39270 AN: 67938

Other (OTH) AF: 0.558 AC: 1174 AN: 2104

Alfa AF: 0.574 Hom.: 119726

Bravo AF: 0.593

Asia WGS AF: 0.495 AC: 1725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.79
DANN	Benign	0.52
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs7953249; hg19: chr12-121403724;