rs855873

Variant names:

• chr1-159077922-A-G
• rs855873
• ENST00000411768.2:c.-20-4403T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-159077922-A-G
• chr1-159077922-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000368129.3(AIM2):​c.-15-11593T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,216 control chromosomes in the GnomAD database, including 56,107 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 0.84 (56107 hom., cov: 33)
• Consequence: AIM2 ENST00000368129.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319
• Publications: 9 publications found

Genes affected

AIM2 (HGNC:357): (absent in melanoma 2) AIM2 is a member of the IFI20X /IFI16 family. It plays a putative role in tumorigenic reversion and may control cell proliferation. Interferon-gamma induces expression of AIM2. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000368129.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AIM2	ENST00000411768.2	TSL:5	c.-20-4403T>C		intron	N/A	ENSP00000512039.1	O14862
	AIM2	ENST00000695580.1		c.-20-4403T>C		intron	N/A	ENSP00000512040.1	O14862
	AIM2	ENST00000913842.1		c.-20-4403T>C		intron	N/A	ENSP00000583901.1

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128299 AN: 152098 Hom.: 56078 Cov.: 33

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.843 AC: 128378 AN: 152216 Hom.: 56107 Cov.: 33 AF XY: 0.848 AC XY: 63111 AN XY: 74428

African (AFR) AF: 0.585 AC: 24271 AN: 41476

American (AMR) AF: 0.908 AC: 13889 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 3191 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5165 AN: 5182

South Asian (SAS) AF: 0.972 AC: 4695 AN: 4830

European-Finnish (FIN) AF: 0.964 AC: 10250 AN: 10628

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63964 AN: 68020

Other (OTH) AF: 0.860 AC: 1817 AN: 2114

Alfa AF: 0.887 Hom.: 35880

Bravo AF: 0.828

Asia WGS AF: 0.959 AC: 3332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.2
DANN	Benign	0.68
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs855873; hg19: chr1-159047712;