rs1002408

Variant names:

• chr1-159120466-T-C
• rs1002408
• ENST00000411768.2:c.-21+1773A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-159120466-T-C
• chr1-159120466-T-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000411768.2(AIM2):​c.-21+1773A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0776 in 152,236 control chromosomes in the GnomAD database, including 1,157 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 0.078 (1157 hom., cov: 32)
• Consequence: AIM2 ENST00000411768.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.778
• Publications: 3 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AIM2	XM_047434808.1	c.-21+1773A>G		intron_variant	Intron 2 of 6		XP_047290764.1
AIM2	XM_047434809.1	c.-124+3054A>G		intron_variant	Intron 3 of 8		XP_047290765.1
AIM2	XR_007064924.1	n.438+1773A>G		intron_variant	Intron 4 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AIM2	ENST00000411768.2	c.-21+1773A>G		intron_variant	Intron 4 of 8	5		ENSP00000512039.1
AIM2	ENST00000695580.1	c.-21+3054A>G		intron_variant	Intron 2 of 6			ENSP00000512040.1
AIM2	ENST00000695579.1	c.-16+11777A>G		intron_variant	Intron 2 of 4			ENSP00000512038.1

Frequencies

GnomAD3 genomes AF: 0.0775 AC: 11787 AN: 152118 Hom.: 1152 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0451

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.00339

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00862

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0776 AC: 11818 AN: 152236 Hom.: 1157 Cov.: 32 AF XY: 0.0763 AC XY: 5679 AN XY: 74452

African (AFR) AF: 0.230 AC: 9528 AN: 41514

American (AMR) AF: 0.0455 AC: 695 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00807 AC: 28 AN: 3470

East Asian (EAS) AF: 0.126 AC: 655 AN: 5180

South Asian (SAS) AF: 0.0267 AC: 129 AN: 4830

European-Finnish (FIN) AF: 0.00339 AC: 36 AN: 10618

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.00862 AC: 586 AN: 68012

Other (OTH) AF: 0.0600 AC: 127 AN: 2116

Alfa AF: 0.0308 Hom.: 587

Bravo AF: 0.0889

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	16
DANN	Benign	0.86
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs1002408; hg19: chr1-159090256;