rs1417806

Variant names:

• chr1-159009401-C-A
• rs1417806
• NM_001364867.2:c.-179-602C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-159009401-C-A
• chr1-159009401-C-G
• chr1-159009401-C-T

Variant summary

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

The NM_001364867.2(IFI16):​c.-179-602C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,066 control chromosomes in the GnomAD database, including 39,659 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 0.72 (39659 hom., cov: 31)
• Consequence: IFI16 NM_001364867.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFI16	NM_001364867.2	c.-179-602C>A		intron_variant	Intron 1 of 12		NP_001351796.1
IFI16	NM_001376588.1	c.-179-602C>A		intron_variant	Intron 1 of 11		NP_001363517.1
IFI16	NM_001376589.1	c.-180+176C>A		intron_variant	Intron 1 of 11		NP_001363518.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFI16	ENST00000447473.6	c.-180+176C>A		intron_variant	Intron 1 of 4	5		ENSP00000407052.2
IFI16	ENST00000426592.6	c.-179-602C>A		intron_variant	Intron 1 of 4	4		ENSP00000406406.2
IFI16	ENST00000566111.5	c.-179-602C>A		intron_variant	Intron 1 of 2	2		ENSP00000458084.1

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109497 AN: 151948 Hom.: 39635 Cov.: 31

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.721 AC: 109571 AN: 152066 Hom.: 39659 Cov.: 31 AF XY: 0.720 AC XY: 53537 AN XY: 74334

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.750

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.697

Alfa AF: 0.709 Hom.: 51444

Bravo AF: 0.728

Asia WGS AF: 0.783 AC: 2720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1417806; hg19: chr1-158979191;