rs10489588

Variant names:

• chr1-3035270-G-A
• rs10489588

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 0.186 in 152,180 control chromosomes in the GnomAD database, including 2,857 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 0.19 (2857 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 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: 0.186 AC: 28293 AN: 152062 Hom.: 2857 Cov.: 33

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.186 AC: 28300 AN: 152180 Hom.: 2857 Cov.: 33 AF XY: 0.184 AC XY: 13689 AN XY: 74398

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.189

Alfa AF: 0.191 Hom.: 1521

Bravo AF: 0.197

Asia WGS AF: 0.229 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489588; hg19: chr1-2951834;