12-68152957-T-C

Variant names:

• chr12-68152957-T-C
• rs3181034
• ENST00000536914.1:n.337-81572T>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.337-81572T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,110 control chromosomes in the GnomAD database, including 43,629 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 (43629 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 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.337-81572T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114187 AN: 151992 Hom.: 43563 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.752 AC: 114314 AN: 152110 Hom.: 43629 Cov.: 32 AF XY: 0.749 AC XY: 55692 AN XY: 74364

African (AFR) AF: 0.864 AC: 35857 AN: 41508

American (AMR) AF: 0.759 AC: 11600 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2692 AN: 3470

East Asian (EAS) AF: 0.667 AC: 3453 AN: 5178

South Asian (SAS) AF: 0.848 AC: 4088 AN: 4822

European-Finnish (FIN) AF: 0.595 AC: 6293 AN: 10570

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47816 AN: 67952

Other (OTH) AF: 0.778 AC: 1644 AN: 2114

Alfa AF: 0.741 Hom.: 6638

Bravo AF: 0.766

Asia WGS AF: 0.796 AC: 2770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.73
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs3181034; hg19: chr12-68546737;