11-86109035-A-G

Variant names:

• chr11-86109035-A-G
• rs543293

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 0.719 in 152,108 control chromosomes in the GnomAD database, including 39,910 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 0.72 (39910 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985
• Publications: 30 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109218 AN: 151990 Hom.: 39868 Cov.: 32

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.719 AC: 109316 AN: 152108 Hom.: 39910 Cov.: 32 AF XY: 0.715 AC XY: 53178 AN XY: 74356

African (AFR) AF: 0.866 AC: 35924 AN: 41496

American (AMR) AF: 0.663 AC: 10128 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2382 AN: 3472

East Asian (EAS) AF: 0.606 AC: 3134 AN: 5174

South Asian (SAS) AF: 0.635 AC: 3059 AN: 4820

European-Finnish (FIN) AF: 0.659 AC: 6961 AN: 10564

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.669 AC: 45491 AN: 67988

Other (OTH) AF: 0.718 AC: 1514 AN: 2110

Alfa AF: 0.683 Hom.: 61465

Bravo AF: 0.725

Asia WGS AF: 0.616 AC: 2141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.77
DANN	Benign	0.49
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs543293; hg19: chr11-85820077;