rs10492198

chr12-68100048-C-T

Variant summary

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

The ENST00000536914.1(IFNG-AS1):n.336+73340C>T 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 0.313 in 151,732 control chromosomes in the GnomAD database, including 9,218 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 0.31 (9218 hom., cov: 31)
• Consequence: IFNG-AS1 ENST00000536914.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 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+73340C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47479 AN: 151614 Hom.: 9209 Cov.: 31

Gnomad AFR AF: 0.0838

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.313 AC: 47491 AN: 151732 Hom.: 9218 Cov.: 31 AF XY: 0.323 AC XY: 23929 AN XY: 74142

Gnomad4 AFR AF: 0.0836

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.334

Alfa AF: 0.343 Hom.: 1279

Bravo AF: 0.306

Asia WGS AF: 0.442 AC: 1533 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.84
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492198; hg19: chr12-68493828;