chr11-13228852-A-G

Variant names:

• chr11-13228852-A-G
• rs10832000

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0875 AC: 3639 AN: 41566

American (AMR) AF: 0.262 AC: 4002 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 761 AN: 3472

East Asian (EAS) AF: 0.148 AC: 765 AN: 5182

South Asian (SAS) AF: 0.205 AC: 993 AN: 4834

European-Finnish (FIN) AF: 0.310 AC: 3285 AN: 10580

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14958 AN: 68006

Other (OTH) AF: 0.181 AC: 382 AN: 2114

Alfa AF: 0.209 Hom.: 14926

Bravo AF: 0.185

Asia WGS AF: 0.180 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.88
DANN	Benign	0.61
PhyloP100		-0.093

Splicing

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

Other links and lift over

dbSNP: rs10832000; hg19: chr11-13250399;