rs2234686

Variant names:

• chr12-68158261-TAAAAAAAA-T
• NM_000619.3:c.115-10_115-3delTTTTTTTT

Your query was ambiguous. Multiple possible variants found:

• chr12-68158261-TAAAAAAAA-T
• chr12-68158261-TAAAAAAAA-TAAAA
• chr12-68158261-TAAAAAAAA-TAAAAA
• chr12-68158261-TAAAAAAAA-TAAAAAA
• chr12-68158261-TAAAAAAAA-TAAAAAAA
• chr12-68158261-TAAAAAAAA-TAAAAAAAAA
• chr12-68158261-TAAAAAAAA-TAAAAAAAAAA
• chr12-68158261-TAAAAAAAA-TAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000619.3(IFNG):​c.115-10_115-3delTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000828 in 1,208,144 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 8.3e-7 (0 hom.)
• Consequence: IFNG NM_000619.3 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.416

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

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNG	NM_000619.3	c.115-10_115-3delTTTTTTTT		splice_region_variant, intron_variant	Intron 1 of 3	ENST00000229135.4	NP_000610.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNG	ENST00000229135.4	c.115-10_115-3delTTTTTTTT		splice_region_variant, intron_variant	Intron 1 of 3	1	NM_000619.3	ENSP00000229135.3
IFNG-AS1	ENST00000536914.1	n.337-76267_337-76260delAAAAAAAA		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 8.28e-7 AC: 1 AN: 1208144 Hom.: 0 AF XY: 0.00000166 AC XY: 1 AN XY: 602032

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000200

GnomAD4 genome Cov.: 0

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr12-68552041;