12-68146965-A-G

Variant names:

• chr12-68146965-A-G
• rs2098395
• ENST00000536914.1:n.337-87564A>G

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-87564A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 152,192 control chromosomes in the GnomAD database, including 53,224 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 0.83 (53224 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 4 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=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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.337-87564A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.830 AC: 126200 AN: 152074 Hom.: 53156 Cov.: 32

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.830 AC: 126330 AN: 152192 Hom.: 53224 Cov.: 32 AF XY: 0.831 AC XY: 61859 AN XY: 74400

African (AFR) AF: 0.960 AC: 39877 AN: 41554

American (AMR) AF: 0.821 AC: 12545 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3038 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5169 AN: 5186

South Asian (SAS) AF: 0.926 AC: 4458 AN: 4814

European-Finnish (FIN) AF: 0.715 AC: 7557 AN: 10570

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50949 AN: 67996

Other (OTH) AF: 0.837 AC: 1765 AN: 2108

Alfa AF: 0.712 Hom.: 2567

Bravo AF: 0.844

Asia WGS AF: 0.954 AC: 3319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.25
DANN	Benign	0.29
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2098395; hg19: chr12-68540745;