rs12003093

Variant names:

• chr9-32588260-A-G
• rs12003093

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 0.319 in 152,126 control chromosomes in the GnomAD database, including 9,331 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 0.32 (9331 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 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: 0.319 AC: 48490 AN: 152008 Hom.: 9283 Cov.: 33

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0887

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.319 AC: 48596 AN: 152126 Hom.: 9331 Cov.: 33 AF XY: 0.315 AC XY: 23397 AN XY: 74386

African (AFR) AF: 0.543 AC: 22527 AN: 41474

American (AMR) AF: 0.251 AC: 3844 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1032 AN: 3470

East Asian (EAS) AF: 0.0891 AC: 462 AN: 5184

South Asian (SAS) AF: 0.220 AC: 1058 AN: 4818

European-Finnish (FIN) AF: 0.263 AC: 2785 AN: 10594

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16039 AN: 67974

Other (OTH) AF: 0.271 AC: 573 AN: 2112

Alfa AF: 0.264 Hom.: 6628

Bravo AF: 0.327

Asia WGS AF: 0.161 AC: 561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.65
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs12003093; hg19: chr9-32588258;