rs11117432

Variant names:

• chr16-85985665-G-A
• rs11117432

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 0.149 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0407

Gnomad4 AMR AF: 0.0910

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.0794

Gnomad4 SAS AF: 0.0793

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.131

Alfa AF: 0.202 Hom.: 4531

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11117432; hg19: chr16-86019271;