rs2069732

Variant names:

• chr12-68160681-A-G
• rs2069732
• ENST00000536914.1:n.337-73848A>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.337-73848A>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
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0716 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.337-73848A>G		intron	N/A

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

African (AFR) AF: 0.00645 AC: 267 AN: 41412

American (AMR) AF: 0.0752 AC: 1143 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.0237 AC: 82 AN: 3466

East Asian (EAS) AF: 0.000582 AC: 3 AN: 5154

South Asian (SAS) AF: 0.0231 AC: 111 AN: 4804

European-Finnish (FIN) AF: 0.0343 AC: 362 AN: 10550

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0344 AC: 2333 AN: 67904

Other (OTH) AF: 0.0343 AC: 72 AN: 2100

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.89
PhyloP100		-0.46
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2069732; hg19: chr12-68554461;