12-68161968-A-T

Variant names:

• chr12-68161968-A-T
• rs7139169
• ENST00000536914.1:n.337-72561A>T

Variant summary

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

The ENST00000536914.1(IFNG-AS1):​n.337-72561A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 151,944 control chromosomes in the GnomAD database, including 41,043 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 0.73 (41043 hom., cov: 30)
• Consequence: IFNG-AS1 ENST00000536914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNG-AS1	ENST00000536914.1	n.337-72561A>T		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111027 AN: 151826 Hom.: 40990 Cov.: 30

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.731 AC: 111142 AN: 151944 Hom.: 41043 Cov.: 30 AF XY: 0.730 AC XY: 54187 AN XY: 74256

African (AFR) AF: 0.788 AC: 32686 AN: 41458

American (AMR) AF: 0.749 AC: 11428 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2694 AN: 3470

East Asian (EAS) AF: 0.717 AC: 3697 AN: 5156

South Asian (SAS) AF: 0.850 AC: 4097 AN: 4818

European-Finnish (FIN) AF: 0.594 AC: 6252 AN: 10530

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47825 AN: 67944

Other (OTH) AF: 0.756 AC: 1596 AN: 2112

Alfa AF: 0.702 Hom.: 4691

Bravo AF: 0.743

Asia WGS AF: 0.808 AC: 2809 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.76
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs7139169; hg19: chr12-68555748;