11-86100196-A-G

Variant names:

• chr11-86100196-A-G
• rs542126

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 0.681 in 152,100 control chromosomes in the GnomAD database, including 36,007 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 0.68 (36007 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 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: 0.681 AC: 103543 AN: 151980 Hom.: 35972 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.681 AC: 103633 AN: 152100 Hom.: 36007 Cov.: 32 AF XY: 0.676 AC XY: 50228 AN XY: 74342

African (AFR) AF: 0.830 AC: 34444 AN: 41490

American (AMR) AF: 0.633 AC: 9678 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2208 AN: 3470

East Asian (EAS) AF: 0.599 AC: 3098 AN: 5170

South Asian (SAS) AF: 0.547 AC: 2636 AN: 4820

European-Finnish (FIN) AF: 0.617 AC: 6526 AN: 10574

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42908 AN: 67968

Other (OTH) AF: 0.676 AC: 1430 AN: 2114

Alfa AF: 0.580 Hom.: 1785

Bravo AF: 0.689

Asia WGS AF: 0.584 AC: 2030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.63
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs542126; hg19: chr11-85811238;