rs12554086

Variant names:

• chr9-80192588-G-A
• rs12554086

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 0.276 in 151,936 control chromosomes in the GnomAD database, including 6,773 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 0.28 (6773 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 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: 0.277 AC: 41995 AN: 151818 Hom.: 6774 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.276 AC: 41992 AN: 151936 Hom.: 6773 Cov.: 32 AF XY: 0.275 AC XY: 20405 AN XY: 74240

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.0398

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.319

Alfa AF: 0.341 Hom.: 13855

Bravo AF: 0.272

Asia WGS AF: 0.171 AC: 595 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	11
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12554086; hg19: chr9-82807503;