rs2193049

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.757

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2193049; hg19: chr12-68546922;