12-68161968-A-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.850

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.756

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7139169; hg19: chr12-68555748;