rs3026943

Variant names:

• chr1-159162136-A-C
• rs3026943
• ENST00000913842.1:c.-336+25675T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-159162136-A-C
• chr1-159162136-A-G
• chr1-159162136-A-T

Variant summary

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

The ENST00000913842.1(AIM2):​c.-336+25675T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,030 control chromosomes in the GnomAD database, including 25,417 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 0.57 (25417 hom., cov: 32)
• Consequence: AIM2 ENST00000913842.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 8 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000913842.1. 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	ENST00000913842.1		c.-336+25675T>G		intron	N/A	ENSP00000583901.1
	AIM2	ENST00000695582.1		n.33+25675T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87339 AN: 151912 Hom.: 25405 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.575 AC: 87374 AN: 152030 Hom.: 25417 Cov.: 32 AF XY: 0.580 AC XY: 43107 AN XY: 74330

African (AFR) AF: 0.505 AC: 20940 AN: 41454

American (AMR) AF: 0.643 AC: 9830 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1635 AN: 3468

East Asian (EAS) AF: 0.713 AC: 3681 AN: 5162

South Asian (SAS) AF: 0.534 AC: 2575 AN: 4822

European-Finnish (FIN) AF: 0.684 AC: 7236 AN: 10572

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39591 AN: 67966

Other (OTH) AF: 0.563 AC: 1186 AN: 2108

Alfa AF: 0.579 Hom.: 34221

Bravo AF: 0.573

Asia WGS AF: 0.568 AC: 1973 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.7
DANN	Benign	0.67
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs3026943; hg19: chr1-159131926;