1-159077922-A-T

Variant names:

• chr1-159077922-A-T
• rs855873
• ENST00000411768.2:c.-20-4403T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000411768.2(AIM2):​c.-20-4403T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AIM2	XM_047434808.1	c.-20-4403T>A		intron_variant	Intron 2 of 6		XP_047290764.1
AIM2	XM_047434809.1	c.-20-4403T>A		intron_variant	Intron 4 of 8		XP_047290765.1
AIM2	XR_007064924.1	n.542-4403T>A		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>A		intron_variant	Intron 4 of 8	5		ENSP00000512039.1
AIM2	ENST00000695580.1	c.-20-4403T>A		intron_variant	Intron 2 of 6			ENSP00000512040.1
AIM2	ENST00000695579.1	c.-15-11593T>A		intron_variant	Intron 2 of 4			ENSP00000512038.1
AIM2	ENST00000368129.3	c.-15-11593T>A		intron_variant	Intron 1 of 2	2		ENSP00000357111.3

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.8
DANN	Benign	0.76
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;