ENST00000536914.1:n.337-42702G>A

Variant names:

• chr12-68191827-G-A
• rs10492197
• ENST00000536914.1:n.337-42702G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000536914.1(IFNG-AS1):​n.337-42702G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334
• Publications: 4 publications found

Genes affected

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

LOC105369818 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105369818	XR_001749193.2	n.3041-4264G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-42702G>A		intron_variant	Intron 5 of 5	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

African (AFR) AF: 0.222 AC: 9158 AN: 41312

American (AMR) AF: 0.327 AC: 4986 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1570 AN: 3472

East Asian (EAS) AF: 0.151 AC: 776 AN: 5156

South Asian (SAS) AF: 0.349 AC: 1673 AN: 4788

European-Finnish (FIN) AF: 0.350 AC: 3674 AN: 10492

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32086 AN: 67948

Other (OTH) AF: 0.405 AC: 852 AN: 2106

Alfa AF: 0.402 Hom.: 1515

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
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs10492197; hg19: chr12-68585607;