rs9933187

Variant names:

• chr16-48522662-G-T
• rs9933187

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 0.378 in 152,038 control chromosomes in the GnomAD database, including 11,623 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 0.38 (11623 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410

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 (AFR) allele frequency at 95% confidence interval = 0.512 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: 0.378 AC: 57441 AN: 151920 Hom.: 11611 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.378 AC: 57488 AN: 152038 Hom.: 11623 Cov.: 32 AF XY: 0.378 AC XY: 28094 AN XY: 74306

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.365

Alfa AF: 0.326 Hom.: 13816

Bravo AF: 0.389

Asia WGS AF: 0.271 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.2
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9933187; hg19: chr16-48556573;