rs11202585

Variant names:

• chr10-87849022-G-C
• rs11202585

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 0.179 in 151,694 control chromosomes in the GnomAD database, including 2,644 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 0.18 (2644 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 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: 0.179 AC: 27063 AN: 151572 Hom.: 2624 Cov.: 30

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.179 AC: 27126 AN: 151694 Hom.: 2644 Cov.: 30 AF XY: 0.180 AC XY: 13344 AN XY: 74078

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.199

Alfa AF: 0.183 Hom.: 329

Bravo AF: 0.181

Asia WGS AF: 0.281 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	5.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11202585; hg19: chr10-89608779; COSMIC: COSV71550661;