rs10489403

Positions:

• chr1-186783442-A-G

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 0.0644 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

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

Ensembl

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

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.0433

Gnomad4 ASJ AF: 0.0305

Gnomad4 EAS AF: 0.00463

Gnomad4 SAS AF: 0.0265

Gnomad4 FIN AF: 0.0211

Gnomad4 NFE AF: 0.0271

Gnomad4 OTH AF: 0.0568

Alfa AF: 0.0540 Hom.: 71

Bravo AF: 0.0702

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489403; hg19: chr1-186752574;