chr11-86089237-G-A

Variant names:

• chr11-86089237-G-A
• rs561655

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.693 in 152,090 control chromosomes in the GnomAD database, including 37,164 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 0.69 (37164 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 75 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.826 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: 0.693 AC: 105339 AN: 151972 Hom.: 37131 Cov.: 31

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.693 AC: 105430 AN: 152090 Hom.: 37164 Cov.: 31 AF XY: 0.688 AC XY: 51136 AN XY: 74320

African (AFR) AF: 0.833 AC: 34590 AN: 41500

American (AMR) AF: 0.646 AC: 9878 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2243 AN: 3472

East Asian (EAS) AF: 0.505 AC: 2606 AN: 5158

South Asian (SAS) AF: 0.579 AC: 2782 AN: 4808

European-Finnish (FIN) AF: 0.630 AC: 6660 AN: 10566

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.655 AC: 44505 AN: 67978

Other (OTH) AF: 0.687 AC: 1449 AN: 2110

Alfa AF: 0.662 Hom.: 134853

Bravo AF: 0.699

Asia WGS AF: 0.561 AC: 1952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	16
DANN	Benign	0.71
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs561655; hg19: chr11-85800279;