rs722749

Variant names:

• chr12-68106858-C-G
• rs722749
• ENST00000536914.1:n.336+80150C>G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.336+80150C>G		intron_variant	Intron 5 of 5	5

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

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.401

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs722749; hg19: chr12-68500638;