rs11202585

chr10-87849022-G-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;