rs10489845

Positions:

• chr1-159059981-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0357 in 152,150 control chromosomes in the GnomAD database, including 230 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 0.036 (230 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.159059981G>C		intergenic_region
AIM2	XR_001737544.2	n.1271-22C>G		intron_variant
AIM2	XR_001737547.3	n.989-22C>G		intron_variant
AIM2	XR_007064924.1	n.1678-22C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0356 AC: 5418 AN: 152032 Hom.: 229 Cov.: 32

Gnomad AFR AF: 0.0993

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0255

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.0110

Gnomad FIN AF: 0.00982

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.00554

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0357 AC: 5434 AN: 152150 Hom.: 230 Cov.: 32 AF XY: 0.0357 AC XY: 2654 AN XY: 74378

Gnomad4 AFR AF: 0.0992

Gnomad4 AMR AF: 0.0259

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.0601

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.00982

Gnomad4 NFE AF: 0.00554

Gnomad4 OTH AF: 0.0279

Alfa AF: 0.0252 Hom.: 17

Bravo AF: 0.0399

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489845; hg19: chr1-159029771;