rs10491819

Variant names:

• chr9-25982490-A-G
• rs10491819

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 0.13 in 152,104 control chromosomes in the GnomAD database, including 2,563 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 (2563 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 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: 0.130 AC: 19780 AN: 151986 Hom.: 2551 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0598

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.0493

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0324

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.130 AC: 19820 AN: 152104 Hom.: 2563 Cov.: 32 AF XY: 0.132 AC XY: 9833 AN XY: 74354

African (AFR) AF: 0.333 AC: 13794 AN: 41448

American (AMR) AF: 0.0596 AC: 912 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0576 AC: 200 AN: 3472

East Asian (EAS) AF: 0.161 AC: 830 AN: 5162

South Asian (SAS) AF: 0.227 AC: 1092 AN: 4816

European-Finnish (FIN) AF: 0.0493 AC: 522 AN: 10584

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0324 AC: 2206 AN: 68012

Other (OTH) AF: 0.111 AC: 234 AN: 2110

Alfa AF: 0.0531 Hom.: 814

Bravo AF: 0.138

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.69
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs10491819; hg19: chr9-25982488;