12-68161231-G-A

Variant names:

• chr12-68161231-G-A
• rs2069705
• ENST00000536914.1:n.337-73298G>A

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-73298G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,752 control chromosomes in the GnomAD database, including 27,698 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 0.60 (27698 hom., cov: 29)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426
• Publications: 129 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.67 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.337-73298G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90274 AN: 151634 Hom.: 27675 Cov.: 29

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.595 AC: 90342 AN: 151752 Hom.: 27698 Cov.: 29 AF XY: 0.586 AC XY: 43414 AN XY: 74148

African (AFR) AF: 0.562 AC: 23219 AN: 41314

American (AMR) AF: 0.507 AC: 7737 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2518 AN: 3470

East Asian (EAS) AF: 0.240 AC: 1243 AN: 5172

South Asian (SAS) AF: 0.689 AC: 3313 AN: 4806

European-Finnish (FIN) AF: 0.489 AC: 5140 AN: 10502

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 44997 AN: 67930

Other (OTH) AF: 0.633 AC: 1333 AN: 2106

Alfa AF: 0.640 Hom.: 76015

Bravo AF: 0.590

Asia WGS AF: 0.545 AC: 1897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.43
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs2069705; hg19: chr12-68555011;