rs9933429

Positions:

• chr16-26159619-G-A

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 0.241 in 152,040 control chromosomes in the GnomAD database, including 4,814 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 0.24 (4814 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36623 AN: 151920 Hom.: 4812 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.241 AC: 36642 AN: 152040 Hom.: 4814 Cov.: 32 AF XY: 0.246 AC XY: 18253 AN XY: 74322

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.246

Alfa AF: 0.263 Hom.: 11004

Bravo AF: 0.233

Asia WGS AF: 0.248 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9933429; hg19: chr16-26170940;