chr11-135033566-G-A

Variant names:

• chr11-135033566-G-A
• rs12575381

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 0.154 in 152,084 control chromosomes in the GnomAD database, including 1,931 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 0.15 (1931 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23434 AN: 151966 Hom.: 1925 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.0780

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.154 AC: 23470 AN: 152084 Hom.: 1931 Cov.: 33 AF XY: 0.156 AC XY: 11562 AN XY: 74322

African (AFR) AF: 0.186 AC: 7714 AN: 41476

American (AMR) AF: 0.113 AC: 1733 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 397 AN: 3468

East Asian (EAS) AF: 0.243 AC: 1258 AN: 5174

South Asian (SAS) AF: 0.0781 AC: 377 AN: 4828

European-Finnish (FIN) AF: 0.199 AC: 2102 AN: 10556

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9382 AN: 67976

Other (OTH) AF: 0.135 AC: 285 AN: 2112

Alfa AF: 0.144 Hom.: 2391

Bravo AF: 0.152

Asia WGS AF: 0.156 AC: 545 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	0.93
DANN	Benign	0.32
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs12575381; hg19: chr11-134903460;