rs12369470

Positions:

• chr12-68151116-T-C

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-83413T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,252 control chromosomes in the GnomAD database, including 1,760 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 0.12 (1760 hom., cov: 31)
• Consequence: IFNG-AS1 ENST00000536914.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-83413T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17534 AN: 152134 Hom.: 1752 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0407

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.115 AC: 17574 AN: 152252 Hom.: 1760 Cov.: 31 AF XY: 0.123 AC XY: 9188 AN XY: 74448

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.0501

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0407

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0606 Hom.: 272

Bravo AF: 0.130

Asia WGS AF: 0.248 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12369470; hg19: chr12-68544896;