NM_001376587.1:c.1162-92A>C

Variant names:

• chr1-159032432-A-C
• rs861318
• NM_001376587.1:c.1162-92A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001376587.1(IFI16):​c.1162-92A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IFI16 NM_001376587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 13 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001376587.1. 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
	IFI16	NM_001376587.1	MANE Select	c.1162-92A>C		intron	N/A	NP_001363516.1
	IFI16	NM_001364867.2		c.1162-92A>C		intron	N/A	NP_001351796.1
	IFI16	NM_001206567.2		c.994-92A>C		intron	N/A	NP_001193496.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFI16	ENST00000295809.12	TSL:5 MANE Select	c.1162-92A>C		intron	N/A	ENSP00000295809.7
	IFI16	ENST00000368131.8	TSL:1	c.1162-92A>C		intron	N/A	ENSP00000357113.4
	IFI16	ENST00000368132.7	TSL:1	c.1162-92A>C		intron	N/A	ENSP00000357114.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 601646 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 307880

African (AFR) AF: 0.00 AC: 0 AN: 15090

American (AMR) AF: 0.00 AC: 0 AN: 12478

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13228

East Asian (EAS) AF: 0.00 AC: 0 AN: 28278

South Asian (SAS) AF: 0.00 AC: 0 AN: 35046

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38322

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3696

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 425366

Other (OTH) AF: 0.00 AC: 0 AN: 30142

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.6
DANN	Benign	0.81
PhyloP100		-0.31

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: rs861318; hg19: chr1-159002222;