chr12-68158714-A-AGTGT

Position:

• chr12-68158714-A-AGTGT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000619.3(IFNG):​c.115-459_115-456dupACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.088 (1060 hom., cov: 0)
• Consequence: IFNG NM_000619.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFNG	NM_000619.3	c.115-459_115-456dupACAC		intron_variant		ENST00000229135.4	NP_000610.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFNG	ENST00000229135.4	c.115-459_115-456dupACAC		intron_variant		1	NM_000619.3	ENSP00000229135.3
IFNG-AS1	ENST00000536914.1	n.337-75789_337-75786dupTGTG		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0882 AC: 13111 AN: 148622 Hom.: 1054 Cov.: 0

Gnomad AFR AF: 0.0785

Gnomad AMI AF: 0.00331

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.0912

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

GnomAD4 genome AF: 0.0883 AC: 13137 AN: 148726 Hom.: 1060 Cov.: 0 AF XY: 0.0962 AC XY: 6975 AN XY: 72530

Gnomad4 AFR AF: 0.0785

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0413

Gnomad4 OTH AF: 0.0903

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34079299; hg19: chr12-68552494;