rs10491859

Variant names:

• chr9-1510299-G-A
• rs10491859

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 0.128 in 152,162 control chromosomes in the GnomAD database, including 1,363 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 0.13 (1363 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.792

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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: 0.128 AC: 19520 AN: 152044 Hom.: 1365 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0672

Gnomad SAS AF: 0.0435

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.128 AC: 19525 AN: 152162 Hom.: 1363 Cov.: 33 AF XY: 0.126 AC XY: 9373 AN XY: 74390

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.0674

Gnomad4 SAS AF: 0.0437

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.134

Alfa AF: 0.121 Hom.: 202

Bravo AF: 0.132

Asia WGS AF: 0.0560 AC: 197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491859; hg19: chr9-1510299;