rs16929092

Variant names:

• chr9-12520709-C-A
• rs16929092

Your query was ambiguous. Multiple possible variants found:

• chr9-12520709-C-A
• chr9-12520709-C-T

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 0.0504 in 146,390 control chromosomes in the GnomAD database, including 306 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 0.050 (306 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.178 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: 0.0506 AC: 7397 AN: 146314 Hom.: 308 Cov.: 29

Gnomad AFR AF: 0.0178

Gnomad AMI AF: 0.0796

Gnomad AMR AF: 0.0457

Gnomad ASJ AF: 0.0623

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.0434

Gnomad MID AF: 0.0599

Gnomad NFE AF: 0.0514

Gnomad OTH AF: 0.0487

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

GnomAD4 genome AF: 0.0504 AC: 7380 AN: 146390 Hom.: 306 Cov.: 29 AF XY: 0.0537 AC XY: 3817 AN XY: 71030

Gnomad4 AFR AF: 0.0178

Gnomad4 AMR AF: 0.0456

Gnomad4 ASJ AF: 0.0623

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.0434

Gnomad4 NFE AF: 0.0513

Gnomad4 OTH AF: 0.0487

Alfa AF: 0.0474 Hom.: 36

Bravo AF: 0.0454

Asia WGS AF: 0.189 AC: 651 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.33
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16929092; hg19: chr9-12520709;