rs11190089

Variant names:

• chr10-81485466-T-C
• rs11190089

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 0.204 in 151,904 control chromosomes in the GnomAD database, including 3,396 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 0.20 (3396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.282 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: 0.204 AC: 30965 AN: 151786 Hom.: 3390 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.204 AC: 30999 AN: 151904 Hom.: 3396 Cov.: 32 AF XY: 0.207 AC XY: 15360 AN XY: 74246

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.188

Alfa AF: 0.215 Hom.: 4040

Bravo AF: 0.206

Asia WGS AF: 0.175 AC: 609 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.5
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11190089; hg19: chr10-83245222;