rs1002408

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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 -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/exons	MANE	UniProt
AIM2	XM_047434808.1	c.-21+1773A>G		intron_variant
AIM2	XM_047434809.1	c.-124+3054A>G		intron_variant
AIM2	XR_007064924.1	n.438+1773A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AIM2	ENST00000368129.3	c.-16+19965A>G		intron_variant		2
AIM2	ENST00000411768.2	c.-21+1773A>G		intron_variant		5		P1
AIM2	ENST00000695579.1	c.-16+11777A>G		intron_variant

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

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.0455

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.0267

Gnomad4 FIN AF: 0.00339

Gnomad4 NFE AF: 0.00862

Gnomad4 OTH AF: 0.0600

Alfa AF: 0.0212 Hom.: 251

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1002408; hg19: chr1-159090256;