chr9-12520709-C-A

Variant names:

• chr9-12520709-C-A
• rs16929092

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 0.0504 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0178 AC: 708 AN: 39856

American (AMR) AF: 0.0456 AC: 660 AN: 14472

Ashkenazi Jewish (ASJ) AF: 0.0623 AC: 213 AN: 3418

East Asian (EAS) AF: 0.183 AC: 921 AN: 5044

South Asian (SAS) AF: 0.188 AC: 877 AN: 4658

European-Finnish (FIN) AF: 0.0434 AC: 393 AN: 9060

Middle Eastern (MID) AF: 0.0530 AC: 14 AN: 264

European-Non Finnish (NFE) AF: 0.0513 AC: 3423 AN: 66682

Other (OTH) AF: 0.0487 AC: 99 AN: 2032

Alfa AF: 0.0516 Hom.: 135

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
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs16929092; hg19: chr9-12520709;