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 ENST00000411768.2(AIM2):​c.-20-4403T>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 ENST00000411768.2 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AIM2	XM_047434808.1	c.-20-4403T>C		intron_variant	Intron 2 of 6		XP_047290764.1
AIM2	XM_047434809.1	c.-20-4403T>C		intron_variant	Intron 4 of 8		XP_047290765.1
AIM2	XR_007064924.1	n.542-4403T>C		intron_variant	Intron 5 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AIM2	ENST00000411768.2	c.-20-4403T>C		intron_variant	Intron 4 of 8	5		ENSP00000512039.1
AIM2	ENST00000695580.1	c.-20-4403T>C		intron_variant	Intron 2 of 6			ENSP00000512040.1
AIM2	ENST00000695579.1	c.-15-11593T>C		intron_variant	Intron 2 of 4			ENSP00000512038.1
AIM2	ENST00000368129.3	c.-15-11593T>C		intron_variant	Intron 1 of 2	2		ENSP00000357111.3

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 v4.3

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;