rs10490067

Variant names:

• chr2-60217740-A-G
• rs10490067

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 0.0714 in 152,064 control chromosomes in the GnomAD database, including 782 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 0.071 (782 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.846
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 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: 0.0713 AC: 10835 AN: 151944 Hom.: 783 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0279

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.0341

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0213

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0714 AC: 10858 AN: 152064 Hom.: 782 Cov.: 32 AF XY: 0.0700 AC XY: 5206 AN XY: 74330

African (AFR) AF: 0.187 AC: 7760 AN: 41468

American (AMR) AF: 0.0279 AC: 426 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3470

East Asian (EAS) AF: 0.123 AC: 635 AN: 5162

South Asian (SAS) AF: 0.0226 AC: 109 AN: 4816

European-Finnish (FIN) AF: 0.0341 AC: 360 AN: 10564

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0213 AC: 1447 AN: 67988

Other (OTH) AF: 0.0544 AC: 115 AN: 2114

Alfa AF: 0.0352 Hom.: 1033

Bravo AF: 0.0763

Asia WGS AF: 0.0720 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.49
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs10490067; hg19: chr2-60444875;