1-159059981-G-C

Variant names:

• chr1-159059981-G-C
• rs10489845
• ENST00000850621.1:n.*85-22C>G

Variant summary

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

The ENST00000850621.1(AIM2):​n.*85-22C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0357 in 152,150 control chromosomes in the GnomAD database, including 230 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 0.036 (230 hom., cov: 32)
• Consequence: AIM2 ENST00000850621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0967 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850621.1. 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	ENST00000850621.1		n.*85-22C>G		intron	N/A	ENSP00000520906.1	O14862

Frequencies

GnomAD3 genomes AF: 0.0356 AC: 5418 AN: 152032 Hom.: 229 Cov.: 32

Gnomad AFR AF: 0.0993

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0255

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.0110

Gnomad FIN AF: 0.00982

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.00554

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0357 AC: 5434 AN: 152150 Hom.: 230 Cov.: 32 AF XY: 0.0357 AC XY: 2654 AN XY: 74378

African (AFR) AF: 0.0992 AC: 4116 AN: 41486

American (AMR) AF: 0.0259 AC: 396 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3470

East Asian (EAS) AF: 0.0601 AC: 311 AN: 5172

South Asian (SAS) AF: 0.0112 AC: 54 AN: 4814

European-Finnish (FIN) AF: 0.00982 AC: 104 AN: 10586

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.00554 AC: 377 AN: 68014

Other (OTH) AF: 0.0279 AC: 59 AN: 2116

Alfa AF: 0.0252 Hom.: 17

Bravo AF: 0.0399

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.68
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10489845; hg19: chr1-159029771;