9-12520709-C-A

Position:

• chr9-12520709-C-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 0.0504 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;