rs11117432

Variant names:

• chr16-85985665-G-A
• rs11117432

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 0.149 in 150,468 control chromosomes in the GnomAD database, including 2,269 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 0.15 (2269 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 42 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 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: 0.149 AC: 22357 AN: 150354 Hom.: 2269 Cov.: 31

Gnomad AFR AF: 0.0408

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0914

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0792

Gnomad SAS AF: 0.0794

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.149 AC: 22360 AN: 150468 Hom.: 2269 Cov.: 31 AF XY: 0.148 AC XY: 10823 AN XY: 73328

African (AFR) AF: 0.0407 AC: 1678 AN: 41242

American (AMR) AF: 0.0910 AC: 1384 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3470

East Asian (EAS) AF: 0.0794 AC: 410 AN: 5162

South Asian (SAS) AF: 0.0793 AC: 379 AN: 4780

European-Finnish (FIN) AF: 0.277 AC: 2685 AN: 9704

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15067 AN: 67616

Other (OTH) AF: 0.131 AC: 274 AN: 2086

Alfa AF: 0.199 Hom.: 10276

Bravo AF: 0.131

Asia WGS AF: 0.0870 AC: 302 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.8
DANN	Benign	0.81
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs11117432; hg19: chr16-86019271;