rs1558744

Positions:

• chr12-68110812-G-A

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.336+84104G>A 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 0.405 in 151,956 control chromosomes in the GnomAD database, including 13,208 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 0.40 (13208 hom., cov: 31)
• Consequence: IFNG-AS1 ENST00000536914.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 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.336+84104G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61455 AN: 151838 Hom.: 13194 Cov.: 31

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.405 AC: 61502 AN: 151956 Hom.: 13208 Cov.: 31 AF XY: 0.395 AC XY: 29348 AN XY: 74270

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.400

Alfa AF: 0.387 Hom.: 17864

Bravo AF: 0.404

Asia WGS AF: 0.201 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1558744; hg19: chr12-68504592;