chr12-67992086-G-A

Variant names:

• chr12-67992086-G-A
• rs10492201
• ENST00000538665.6:n.133+2507G>A

Variant summary

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

The ENST00000538665.6(IFNG-AS1):​n.133+2507G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,076 control chromosomes in the GnomAD database, including 1,158 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 0.11 (1158 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000538665.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 1 publications found

Genes affected

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

LINC01479 (HGNC:51123): (long intergenic non-protein coding RNA 1479)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000538665.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNG-AS1	NR_104125.3	MANE Select	n.133+2507G>A		intron	N/A
	IFNG-AS1	NR_104124.3		n.133+2507G>A		intron	N/A
	IFNG-AS1	NR_186227.2		n.133+2507G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNG-AS1	ENST00000538665.6	TSL:2 MANE Select	n.133+2507G>A		intron	N/A
	IFNG-AS1	ENST00000536914.1	TSL:5	n.51+2507G>A		intron	N/A
	IFNG-AS1	ENST00000541715.5	TSL:3	n.124+2507G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16469 AN: 151958 Hom.: 1156 Cov.: 32

Gnomad AFR AF: 0.0350

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0825

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.0900

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

GnomAD4 genome AF: 0.108 AC: 16464 AN: 152076 Hom.: 1158 Cov.: 32 AF XY: 0.108 AC XY: 8011 AN XY: 74334

African (AFR) AF: 0.0349 AC: 1449 AN: 41492

American (AMR) AF: 0.149 AC: 2281 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0825 AC: 286 AN: 3468

East Asian (EAS) AF: 0.235 AC: 1220 AN: 5182

South Asian (SAS) AF: 0.161 AC: 775 AN: 4812

European-Finnish (FIN) AF: 0.105 AC: 1113 AN: 10560

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9128 AN: 67970

Other (OTH) AF: 0.0890 AC: 188 AN: 2112

Alfa AF: 0.115 Hom.: 978

Bravo AF: 0.110

Asia WGS AF: 0.140 AC: 484 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.76
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs10492201; hg19: chr12-68385866;