chr1-159032432-A-G

Position:

• chr1-159032432-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001376587.1(IFI16):​c.1162-92A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 750,968 control chromosomes in the GnomAD database, including 223,809 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 0.70 (40261 hom., cov: 31)
  • Exomes 𝑓: 0.78 (183548 hom.)
• Consequence: IFI16 NM_001376587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

Genes affected

IFI16 (HGNC:5395): (interferon gamma inducible protein 16) This gene encodes a member of the HIN-200 (hematopoietic interferon-inducible nuclear antigens with 200 amino acid repeats) family of cytokines. The encoded protein contains domains involved in DNA binding, transcriptional regulation, and protein-protein interactions. The protein localizes to the nucleoplasm and nucleoli, and interacts with p53 and retinoblastoma-1. It modulates p53 function, and inhibits cell growth in the Ras/Raf signaling pathway. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2011]

IFI16 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFI16	NM_001376587.1	c.1162-92A>G		intron_variant		ENST00000295809.12	NP_001363516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFI16	ENST00000295809.12	c.1162-92A>G		intron_variant		5	NM_001376587.1	ENSP00000295809.7

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106783 AN: 152028 Hom.: 40248 Cov.: 31

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.737

GnomAD4 exome AF: 0.778 AC: 465789 AN: 598822 Hom.: 183548 AF XY: 0.777 AC XY: 238122 AN XY: 306348

Gnomad4 AFR exome AF: 0.366

Gnomad4 AMR exome AF: 0.839

Gnomad4 ASJ exome AF: 0.805

Gnomad4 EAS exome AF: 0.686

Gnomad4 SAS exome AF: 0.683

Gnomad4 FIN exome AF: 0.839

Gnomad4 NFE exome AF: 0.800

Gnomad4 OTH exome AF: 0.758

GnomAD4 genome AF: 0.702 AC: 106836 AN: 152146 Hom.: 40261 Cov.: 31 AF XY: 0.708 AC XY: 52679 AN XY: 74378

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.719

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.821

Gnomad4 OTH AF: 0.740

Alfa AF: 0.802 Hom.: 48064

Bravo AF: 0.691

Asia WGS AF: 0.661 AC: 2298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.8
DANN	Benign	0.83

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

Other links and lift over

dbSNP: rs861318; hg19: chr1-159002222; COSMIC: COSV55535389; COSMIC: COSV55535389;