rs3026943

Variant names:

• chr1-159162136-A-C
• rs3026943
• ENST00000695582.1:n.33+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. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000695582.1(AIM2):​n.33+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 ENST00000695582.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AIM2	ENST00000695582.1	n.33+25675T>G		intron_variant	Intron 1 of 3

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

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.563

Alfa AF: 0.580 Hom.: 26412

Bravo AF: 0.573

Asia WGS AF: 0.568 AC: 1973 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3026943; hg19: chr1-159131926;