rs2069732

Variant names:

• chr12-68160681-A-G
• rs2069732
• ENST00000536914.1:n.337-73848A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000536914.1(IFNG-AS1):​n.337-73848A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0288 in 151,796 control chromosomes in the GnomAD database, including 115 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 0.029 (115 hom., cov: 30)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0716 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.337-73848A>G		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.0289 AC: 4385 AN: 151678 Hom.: 116 Cov.: 30

Gnomad AFR AF: 0.00647

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0756

Gnomad ASJ AF: 0.0237

Gnomad EAS AF: 0.000581

Gnomad SAS AF: 0.0233

Gnomad FIN AF: 0.0343

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0344

Gnomad OTH AF: 0.0346

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

GnomAD4 genome AF: 0.0288 AC: 4378 AN: 151796 Hom.: 115 Cov.: 30 AF XY: 0.0294 AC XY: 2181 AN XY: 74204

Gnomad4 AFR AF: 0.00645

Gnomad4 AMR AF: 0.0752

Gnomad4 ASJ AF: 0.0237

Gnomad4 EAS AF: 0.000582

Gnomad4 SAS AF: 0.0231

Gnomad4 FIN AF: 0.0343

Gnomad4 NFE AF: 0.0344

Gnomad4 OTH AF: 0.0343

Alfa AF: 0.0334 Hom.: 21

Bravo AF: 0.0318

Asia WGS AF: 0.00924 AC: 32 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2069732; hg19: chr12-68554461;