rs12529093

Variant names:

• chr6-32448081-A-G
• rs12529093

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 0.127 in 152,204 control chromosomes in the GnomAD database, including 1,422 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 0.13 (1422 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 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: 0.127 AC: 19309 AN: 152086 Hom.: 1422 Cov.: 32

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.0425

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.127 AC: 19327 AN: 152204 Hom.: 1422 Cov.: 32 AF XY: 0.130 AC XY: 9696 AN XY: 74388

Gnomad4 AFR AF: 0.0848

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0617

Gnomad4 EAS AF: 0.0424

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.124

Alfa AF: 0.125 Hom.: 427

Bravo AF: 0.116

Asia WGS AF: 0.0980 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12529093; hg19: chr6-32415858;