chr12-68106295-G-A

Variant names:

• chr12-68106295-G-A
• rs7134599
• ENST00000536914.1:n.336+79587G>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.336+79587G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,886 control chromosomes in the GnomAD database, including 8,075 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 0.32 (8075 hom., cov: 32)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 72 publications found

Genes affected

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

ENSG00000301254 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000536914.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNG-AS1	ENST00000536914.1	TSL:5	n.336+79587G>A		intron	N/A
	ENSG00000301254	ENST00000777404.1		n.168-10324C>T		intron	N/A
	ENSG00000301254	ENST00000777405.1		n.188-10324C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47976 AN: 151768 Hom.: 8069 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.316 AC: 48003 AN: 151886 Hom.: 8075 Cov.: 32 AF XY: 0.307 AC XY: 22793 AN XY: 74220

African (AFR) AF: 0.293 AC: 12132 AN: 41414

American (AMR) AF: 0.242 AC: 3694 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1126 AN: 3468

East Asian (EAS) AF: 0.00290 AC: 15 AN: 5172

South Asian (SAS) AF: 0.125 AC: 602 AN: 4822

European-Finnish (FIN) AF: 0.327 AC: 3440 AN: 10512

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.382 AC: 25973 AN: 67944

Other (OTH) AF: 0.317 AC: 669 AN: 2110

Alfa AF: 0.351 Hom.: 44797

Bravo AF: 0.309

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.43
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs7134599; hg19: chr12-68500075;