chr12-68158714-AGTGT-A

Variant names:

• chr12-68158714-AGTGT-A
• rs34079299
• NM_000619.3:c.115-459_115-456delACAC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_000619.3(IFNG):​c.115-459_115-456delACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: 𝑓 0.021 (100 hom., cov: 0)
• Consequence: IFNG NM_000619.3 intron
• Clinical Significance: risk factor no assertion criteria provided O:2
• Conservation: PhyloP100: 0.144
• Publications: 0 publications found

Genes affected

IFNG (HGNC:5438): (interferon gamma) This gene encodes a soluble cytokine that is a member of the type II interferon class. The encoded protein is secreted by cells of both the innate and adaptive immune systems. The active protein is a homodimer that binds to the interferon gamma receptor which triggers a cellular response to viral and microbial infections. Mutations in this gene are associated with an increased susceptibility to viral, bacterial and parasitic infections and to several autoimmune diseases. [provided by RefSeq, Dec 2015]

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

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0594 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000619.3. 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	NM_000619.3	MANE Select	c.115-459_115-456delACAC		intron	N/A	NP_000610.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNG	ENST00000229135.4	TSL:1 MANE Select	c.115-459_115-456delACAC		intron	N/A	ENSP00000229135.3
	IFNG-AS1	ENST00000536914.1	TSL:5	n.337-75814_337-75811delGTGT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0214 AC: 3177 AN: 148620 Hom.: 99 Cov.: 0

Gnomad AFR AF: 0.0614

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00872

Gnomad ASJ AF: 0.00233

Gnomad EAS AF: 0.000989

Gnomad SAS AF: 0.00171

Gnomad FIN AF: 0.0393

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.00167

Gnomad OTH AF: 0.0190

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

GnomAD4 genome AF: 0.0214 AC: 3186 AN: 148724 Hom.: 100 Cov.: 0 AF XY: 0.0222 AC XY: 1613 AN XY: 72528

African (AFR) AF: 0.0615 AC: 2491 AN: 40534

American (AMR) AF: 0.00877 AC: 131 AN: 14930

Ashkenazi Jewish (ASJ) AF: 0.00233 AC: 8 AN: 3438

East Asian (EAS) AF: 0.000991 AC: 5 AN: 5046

South Asian (SAS) AF: 0.00171 AC: 8 AN: 4672

European-Finnish (FIN) AF: 0.0393 AC: 391 AN: 9948

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.00167 AC: 112 AN: 66886

Other (OTH) AF: 0.0188 AC: 39 AN: 2072

Alfa AF: 0.00513 Hom.: 431

ClinVar

ClinVar submissions as Germline

Significance: risk factor

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Aplastic anemia, susceptibility to (1)
-	-	-	Tsc2 angiomyolipomas, renal, modifier of (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs34079299; hg19: chr12-68552494;