rs10492197

Positions:

• chr12-68191827-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.337-42702G>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 0.365 in 151,726 control chromosomes in the GnomAD database, including 11,133 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 0.37 (11133 hom., cov: 31)
• Consequence: IFNG-AS1 ENST00000536914.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334

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	UniProt
LOC105369818	XR_001749193.2	n.3041-4264G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-42702G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55382 AN: 151606 Hom.: 11124 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.365 AC: 55393 AN: 151726 Hom.: 11133 Cov.: 31 AF XY: 0.357 AC XY: 26496 AN XY: 74128

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.405

Alfa AF: 0.409 Hom.: 1491

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	6.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492197; hg19: chr12-68585607;