chr12-68106858-C-G

Variant names:

• chr12-68106858-C-G
• rs722749
• ENST00000536914.1:n.336+80150C>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.336+80150C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,996 control chromosomes in the GnomAD database, including 13,242 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 0.41 (13242 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 8 publications found

Genes affected

IFNG-AS1 (HGNC:43910): (IFNG antisense RNA 1)

ENSG00000301254 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 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.336+80150C>G		intron	N/A
	ENSG00000301254	ENST00000777404.1		n.168-10887G>C		intron	N/A
	ENSG00000301254	ENST00000777405.1		n.188-10887G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61588 AN: 151878 Hom.: 13229 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.405 AC: 61634 AN: 151996 Hom.: 13242 Cov.: 32 AF XY: 0.396 AC XY: 29411 AN XY: 74282

African (AFR) AF: 0.522 AC: 21650 AN: 41448

American (AMR) AF: 0.294 AC: 4484 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1214 AN: 3468

East Asian (EAS) AF: 0.118 AC: 612 AN: 5172

South Asian (SAS) AF: 0.188 AC: 908 AN: 4820

European-Finnish (FIN) AF: 0.382 AC: 4039 AN: 10560

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.405 AC: 27506 AN: 67952

Other (OTH) AF: 0.401 AC: 847 AN: 2112

Alfa AF: 0.411 Hom.: 1607

Bravo AF: 0.405

Asia WGS AF: 0.206 AC: 720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.70
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs722749; hg19: chr12-68500638;