12-68153142-C-G

Variant names:

• chr12-68153142-C-G
• rs2193049
• ENST00000536914.1:n.337-81387C>G

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-81387C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,076 control chromosomes in the GnomAD database, including 41,516 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 0.73 (41516 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 8 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.824 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
IFNG-AS1	ENST00000536914.1	n.337-81387C>G		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111502 AN: 151958 Hom.: 41449 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.734 AC: 111630 AN: 152076 Hom.: 41516 Cov.: 32 AF XY: 0.732 AC XY: 54430 AN XY: 74322

African (AFR) AF: 0.823 AC: 34119 AN: 41474

American (AMR) AF: 0.741 AC: 11336 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2689 AN: 3466

East Asian (EAS) AF: 0.636 AC: 3294 AN: 5176

South Asian (SAS) AF: 0.845 AC: 4078 AN: 4824

European-Finnish (FIN) AF: 0.593 AC: 6259 AN: 10554

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47397 AN: 67980

Other (OTH) AF: 0.757 AC: 1595 AN: 2108

Alfa AF: 0.702 Hom.: 4682

Bravo AF: 0.747

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.61
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs2193049; hg19: chr12-68546922;