rs2486489

Variant names:

• chr10-58316293-T-G
• rs2486489

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0403 in 152,188 control chromosomes in the GnomAD database, including 232 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 0.040 (232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0956 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

Frequencies

GnomAD3 genomes AF: 0.0402 AC: 6119 AN: 152070 Hom.: 231 Cov.: 32

Gnomad AFR AF: 0.0980

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0214

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0498

Gnomad FIN AF: 0.00188

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0185

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0403 AC: 6132 AN: 152188 Hom.: 232 Cov.: 32 AF XY: 0.0404 AC XY: 3003 AN XY: 74420

African (AFR) AF: 0.0981 AC: 4072 AN: 41508

American (AMR) AF: 0.0213 AC: 326 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3468

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5174

South Asian (SAS) AF: 0.0494 AC: 238 AN: 4816

European-Finnish (FIN) AF: 0.00188 AC: 20 AN: 10622

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0185 AC: 1256 AN: 68002

Other (OTH) AF: 0.0351 AC: 74 AN: 2110

Alfa AF: 0.0347 Hom.: 33

Bravo AF: 0.0429

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.67
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2486489; hg19: chr10-60076053;