11-86100196-A-G

Position:

• chr11-86100196-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.676

Alfa AF: 0.556 Hom.: 1511

Bravo AF: 0.689

Asia WGS AF: 0.584 AC: 2030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs542126; hg19: chr11-85811238;