rs12529093

Positions:

• chr6-32448081-A-G

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/exons	MANE	UniProt

Ensembl

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