rs2069705

Positions:

• chr12-68161231-G-A
• chr12-68161231-G-C

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-73298G>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 0.595 in 151,752 control chromosomes in the GnomAD database, including 27,698 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 0.60 (27698 hom., cov: 29)
• Consequence: IFNG-AS1 ENST00000536914.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.67 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.337-73298G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90274 AN: 151634 Hom.: 27675 Cov.: 29

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.595 AC: 90342 AN: 151752 Hom.: 27698 Cov.: 29 AF XY: 0.586 AC XY: 43414 AN XY: 74148

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.633

Alfa AF: 0.645 Hom.: 30652

Bravo AF: 0.590

Asia WGS AF: 0.545 AC: 1897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2069705; hg19: chr12-68555011;