chr12-68154443-T-C

Variant names:

• chr12-68154443-T-C
• rs2069727
• ENST00000536914.1:n.337-80086T>C

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-80086T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,952 control chromosomes in the GnomAD database, including 10,768 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 0.36 (10768 hom., cov: 31)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876
• Publications: 88 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNG-AS1	ENST00000536914.1	TSL:5	n.337-80086T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54234 AN: 151834 Hom.: 10761 Cov.: 31

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.357 AC: 54245 AN: 151952 Hom.: 10768 Cov.: 31 AF XY: 0.350 AC XY: 26023 AN XY: 74250

African (AFR) AF: 0.205 AC: 8499 AN: 41456

American (AMR) AF: 0.323 AC: 4939 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1539 AN: 3472

East Asian (EAS) AF: 0.156 AC: 804 AN: 5158

South Asian (SAS) AF: 0.388 AC: 1865 AN: 4802

European-Finnish (FIN) AF: 0.341 AC: 3590 AN: 10534

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31559 AN: 67948

Other (OTH) AF: 0.399 AC: 842 AN: 2110

Alfa AF: 0.435 Hom.: 27063

Bravo AF: 0.346

Asia WGS AF: 0.345 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.12
DANN	Benign	0.62
PhyloP100		-0.88

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2069727;

hg19: chr12-68548223;