rs10832000

Variant names:

• chr11-13228852-A-G
• rs10832000

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;