rs2069728

Variant names:

• chr12-68154004-C-T
• rs2069728
• ENST00000536914.1:n.337-80525C>T

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-80525C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,172 control chromosomes in the GnomAD database, including 1,831 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 0.13 (1831 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 24 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 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.337-80525C>T		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19362 AN: 152052 Hom.: 1829 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0877

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0851

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.0522

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.0657

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.127 AC: 19381 AN: 152172 Hom.: 1831 Cov.: 32 AF XY: 0.129 AC XY: 9572 AN XY: 74396

African (AFR) AF: 0.255 AC: 10589 AN: 41492

American (AMR) AF: 0.0876 AC: 1339 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 445 AN: 3470

East Asian (EAS) AF: 0.0855 AC: 443 AN: 5182

South Asian (SAS) AF: 0.251 AC: 1210 AN: 4812

European-Finnish (FIN) AF: 0.0522 AC: 554 AN: 10606

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.0656 AC: 4465 AN: 68014

Other (OTH) AF: 0.117 AC: 246 AN: 2110

Alfa AF: 0.113 Hom.: 481

Bravo AF: 0.132

Asia WGS AF: 0.162 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.21
DANN	Benign	0.60
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs2069728; hg19: chr12-68547784;