rs10491859

Variant names:

• chr9-1510299-G-A
• rs10491859

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 0.128 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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

African (AFR) AF: 0.176 AC: 7299 AN: 41496

American (AMR) AF: 0.104 AC: 1589 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3472

East Asian (EAS) AF: 0.0674 AC: 348 AN: 5166

South Asian (SAS) AF: 0.0437 AC: 211 AN: 4824

European-Finnish (FIN) AF: 0.104 AC: 1101 AN: 10596

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7849 AN: 68008

Other (OTH) AF: 0.134 AC: 284 AN: 2114

Alfa AF: 0.122 Hom.: 213

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
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs10491859; hg19: chr9-1510299;