rs10489531

Variant names:

• chr1-115240381-G-A
• rs10489531

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 0.24 in 152,106 control chromosomes in the GnomAD database, including 5,714 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 0.24 (5714 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.351 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: 0.240 AC: 36510 AN: 151986 Hom.: 5716 Cov.: 32

Gnomad AFR AF: 0.0721

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.240 AC: 36497 AN: 152106 Hom.: 5714 Cov.: 32 AF XY: 0.233 AC XY: 17341 AN XY: 74330

Gnomad4 AFR AF: 0.0719

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.260

Alfa AF: 0.318 Hom.: 3892

Bravo AF: 0.225

Asia WGS AF: 0.0800 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489531; hg19: chr1-115783002;