rs2870950

Positions:

• chr12-68190926-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.337-43603G>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 0.364 in 151,960 control chromosomes in the GnomAD database, including 11,112 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 0.36 (11112 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243

Genes affected

IFNG-AS1 (HGNC:43910): (IFNG antisense RNA 1)

LOC105369818 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369818	XR_001749193.2	n.3040+4982G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-43603G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55372 AN: 151842 Hom.: 11103 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.364 AC: 55383 AN: 151960 Hom.: 11112 Cov.: 32 AF XY: 0.357 AC XY: 26512 AN XY: 74278

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.404

Alfa AF: 0.393 Hom.: 1813

Bravo AF: 0.354

Asia WGS AF: 0.316 AC: 1098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2870950; hg19: chr12-68584706;