rs11866031

Variant names:

• chr16-86693693-A-G
• rs11866031

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 0.225 in 152,074 control chromosomes in the GnomAD database, including 5,311 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 0.22 (5311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 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: 0.225 AC: 34117 AN: 151956 Hom.: 5292 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0569

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.225 AC: 34186 AN: 152074 Hom.: 5311 Cov.: 32 AF XY: 0.222 AC XY: 16504 AN XY: 74344

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.0564

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.210

Alfa AF: 0.155 Hom.: 1232

Bravo AF: 0.246

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11866031; hg19: chr16-86727299;