rs11117283

Variant names:

• chr16-87537555-C-T
• rs11117283

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 0.491 in 152,082 control chromosomes in the GnomAD database, including 19,781 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 0.49 (19781 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74718 AN: 151964 Hom.: 19785 Cov.: 33

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.491 AC: 74719 AN: 152082 Hom.: 19781 Cov.: 33 AF XY: 0.482 AC XY: 35857 AN XY: 74350

African (AFR) AF: 0.350 AC: 14537 AN: 41492

American (AMR) AF: 0.408 AC: 6234 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1941 AN: 3468

East Asian (EAS) AF: 0.168 AC: 866 AN: 5166

South Asian (SAS) AF: 0.410 AC: 1976 AN: 4818

European-Finnish (FIN) AF: 0.547 AC: 5787 AN: 10588

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.610 AC: 41483 AN: 67958

Other (OTH) AF: 0.531 AC: 1122 AN: 2114

Alfa AF: 0.539 Hom.: 9933

Bravo AF: 0.470

Asia WGS AF: 0.285 AC: 994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.52
DANN	Benign	0.34
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs11117283; hg19: chr16-87571161;