12-68153413-T-G

Variant names:

• chr12-68153413-T-G
• rs2193050
• ENST00000536914.1:n.337-81116T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000536914.1(IFNG-AS1):​n.337-81116T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 152,036 control chromosomes in the GnomAD database, including 43,989 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 0.75 (43989 hom., cov: 31)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 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.337-81116T>G		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114604 AN: 151918 Hom.: 43922 Cov.: 31

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.755 AC: 114732 AN: 152036 Hom.: 43989 Cov.: 31 AF XY: 0.752 AC XY: 55866 AN XY: 74300

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.782

Alfa AF: 0.709 Hom.: 4548

Bravo AF: 0.770

Asia WGS AF: 0.797 AC: 2773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2193050; hg19: chr12-68547193;