rs10489403

Variant names:

• chr1-186783442-A-G
• rs10489403

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 0.0644 in 152,244 control chromosomes in the GnomAD database, including 580 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 0.064 (580 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.671
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0644 AC: 9791 AN: 152126 Hom.: 577 Cov.: 33

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0433

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.0267

Gnomad FIN AF: 0.0211

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0271

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0644 AC: 9798 AN: 152244 Hom.: 580 Cov.: 33 AF XY: 0.0629 AC XY: 4681 AN XY: 74450

African (AFR) AF: 0.159 AC: 6612 AN: 41506

American (AMR) AF: 0.0433 AC: 662 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0305 AC: 106 AN: 3470

East Asian (EAS) AF: 0.00463 AC: 24 AN: 5184

South Asian (SAS) AF: 0.0265 AC: 128 AN: 4822

European-Finnish (FIN) AF: 0.0211 AC: 224 AN: 10626

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0271 AC: 1844 AN: 68028

Other (OTH) AF: 0.0568 AC: 120 AN: 2114

Alfa AF: 0.0569 Hom.: 75

Bravo AF: 0.0702

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.47
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs10489403; hg19: chr1-186752574;