12-68143094-T-C

Variant names:

• chr12-68143094-T-C
• rs2193048

Variant summary

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

The variant allele was found at a frequency of 0.752 in 152,122 control chromosomes in the GnomAD database, including 43,718 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 (43718 hom., cov: 32)
• Consequence: LOC100509370 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 3 publications found

Genes affected

LOC100509370 (HGNC:):

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 = 0.857 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNG-AS1	ENST00000536914.1	TSL:5	n.337-91435T>C		intron	N/A
	ENSG00000256708	ENST00000542812.1	TSL:6	n.-224T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114320 AN: 152004 Hom.: 43652 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.752 AC: 114447 AN: 152122 Hom.: 43718 Cov.: 32 AF XY: 0.750 AC XY: 55751 AN XY: 74352

African (AFR) AF: 0.864 AC: 35895 AN: 41538

American (AMR) AF: 0.758 AC: 11592 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2692 AN: 3468

East Asian (EAS) AF: 0.668 AC: 3447 AN: 5164

South Asian (SAS) AF: 0.848 AC: 4087 AN: 4822

European-Finnish (FIN) AF: 0.596 AC: 6289 AN: 10558

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

European-Non Finnish (NFE) AF: 0.705 AC: 47933 AN: 67970

Other (OTH) AF: 0.777 AC: 1641 AN: 2112

Alfa AF: 0.720 Hom.: 5621

Bravo AF: 0.767

Asia WGS AF: 0.796 AC: 2771 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	2.8
DANN	Benign	0.86
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs2193048; hg19: chr12-68536874;