rs10511563

Variant names:

• chr9-11089482-C-A
• rs10511563

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 0.271 in 151,834 control chromosomes in the GnomAD database, including 5,671 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 0.27 (5671 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 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: 0.271 AC: 41187 AN: 151716 Hom.: 5660 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.271 AC: 41217 AN: 151834 Hom.: 5671 Cov.: 32 AF XY: 0.267 AC XY: 19813 AN XY: 74212

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.295

Alfa AF: 0.281 Hom.: 729

Bravo AF: 0.276

Asia WGS AF: 0.213 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.4
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511563; hg19: chr9-11089482;