rs10832000

chr11-13228852-A-G

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 0.191 in 152,258 control chromosomes in the GnomAD database, including 3,251 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 0.19 (3251 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.255 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: 0.191 AC: 29055 AN: 152140 Hom.: 3246 Cov.: 33

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.191 AC: 29081 AN: 152258 Hom.: 3251 Cov.: 33 AF XY: 0.196 AC XY: 14608 AN XY: 74428

Gnomad4 AFR AF: 0.0875

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.181

Alfa AF: 0.215 Hom.: 7436

Bravo AF: 0.185

Asia WGS AF: 0.180 AC: 629 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	0.88
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10832000; hg19: chr11-13250399;