Genetic Variant IFNG:c.*97_*100delTCAA (chr12-68155252-TTTGA-T) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BS1_SupportingBS2

The NM_000619.3(IFNG):c.*97_*100delTCAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00177 in 760,522 control chromosomes in the GnomAD database, including 9 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: 𝑓 0.0031 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0014 ( 8 hom. )

Consequence

IFNG
NM_000619.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2O:1

Conservation

PhyloP100: 0.908

Variant links:

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 links:

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

IFNG-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

BS1

Variant frequency is greater than expected in population mid. GnomAdExome4 allele frequency = 0.00143 (869/608186) while in subpopulation MID AF = 0.0194 (50/2582). AF 95% confidence interval is 0.0151. There are 8 homozygotes in GnomAdExome4. There are 426 alleles in the male GnomAdExome4 subpopulation. This position FAILED quality control check. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

BS2

High Homozygotes in GnomAdExome4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNG	NM_000619.3 link	c.97_100delTCAA		3_prime_UTR_variant	Exon 4 of 4	ENST00000229135.4	NP_000610.2	P01579A0A7R8GUN6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNG	ENST00000229135 link	c.97_100delTCAA		3_prime_UTR_variant	Exon 4 of 4	1	NM_000619.3	ENSP00000229135.3		P01579
IFNG-AS1	ENST00000536914.1 link	n.337-79271_337-79268delTGAT		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.00314

AC:

478

AN:

152218

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00622

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00622

Gnomad ASJ

AF:

0.0133

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000827

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.000882

Gnomad OTH

AF:

0.00478

GnomAD4 exome

AF:

0.00143

AC:

869

AN:

608186

Hom.:

AF XY:

0.00138

AC XY:

426

AN XY:

309528

show subpopulations

Gnomad4 AFR exome

AF:

0.00755

AC:

106

AN:

14048

Gnomad4 AMR exome

AF:

0.00401

AC:

AN:

13232

Gnomad4 ASJ exome

AF:

0.0102

AC:

137

AN:

13494

Gnomad4 EAS exome

AF:

0.00

AC:

AN:

27950

Gnomad4 SAS exome

AF:

0.000484

AC:

AN:

28920

Gnomad4 FIN exome

AF:

0.0000317

AC:

AN:

31560

Gnomad4 NFE exome

AF:

0.000933

AC:

417

AN:

446726

Gnomad4 Remaining exome

AF:

0.00307

AC:

AN:

29674

Heterozygous variant carriers

124

166

207

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00314

AC:

479

AN:

152336

Hom.:

Cov.:

AF XY:

0.00294

AC XY:

219

AN XY:

74506

show subpopulations

Gnomad4 AFR

AF:

0.00623

AC:

0.00622896

AN:

0.00622896

Gnomad4 AMR

AF:

0.00621

AC:

0.00620996

AN:

0.00620996

Gnomad4 ASJ

AF:

0.0133

AC:

0.0132565

AN:

0.0132565

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.000828

AC:

0.000828157

AN:

0.000828157

Gnomad4 FIN

AF:

0.00

AC:

AN:

Gnomad4 NFE

AF:

0.000882

AC:

0.00088199

AN:

0.00088199

Gnomad4 OTH

AF:

0.00473

AC:

0.0047259

AN:

0.0047259

Heterozygous variant carriers

107

134

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00276

Hom.:

Bravo

AF:

0.00389

Asia WGS

AF:

0.00116

AC:

AN:

3464

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Uncertain:1Other:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Human Evolutionary Genetics, Institut Pasteur

Significance:not provided

Review Status:no classification provided

Collection Method:literature only

- -

Aplastic anemia

Uncertain:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over