12-68232582-G-C

Variant names:

• chr12-68232582-G-C
• rs1125098
• ENST00000536914.1:n.337-1947G>C

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-1947G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,136 control chromosomes in the GnomAD database, including 7,312 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 0.28 (7312 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345
• Publications: 2 publications found

Genes affected

IFNG-AS1 (HGNC:43910): (IFNG antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000536914.1. 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
	IFNG-AS1	ENST00000536914.1	TSL:5	n.337-1947G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42037 AN: 152018 Hom.: 7312 Cov.: 32

Gnomad AFR AF: 0.0901

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.0554

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.276 AC: 42034 AN: 152136 Hom.: 7312 Cov.: 32 AF XY: 0.268 AC XY: 19897 AN XY: 74366

African (AFR) AF: 0.0899 AC: 3735 AN: 41524

American (AMR) AF: 0.299 AC: 4575 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1211 AN: 3464

East Asian (EAS) AF: 0.0557 AC: 289 AN: 5184

South Asian (SAS) AF: 0.253 AC: 1218 AN: 4820

European-Finnish (FIN) AF: 0.235 AC: 2484 AN: 10576

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27462 AN: 67966

Other (OTH) AF: 0.297 AC: 627 AN: 2110

Alfa AF: 0.229 Hom.: 668

Bravo AF: 0.271

Asia WGS AF: 0.174 AC: 609 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.34
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs1125098; hg19: chr12-68626362;