rs12682293

Variant names:

• chr8-30026561-A-C
• rs12682293

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 0.416 in 152,136 control chromosomes in the GnomAD database, including 16,222 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 0.42 (16222 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 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: 0.417 AC: 63320 AN: 152016 Hom.: 16223 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.416 AC: 63325 AN: 152136 Hom.: 16222 Cov.: 33 AF XY: 0.414 AC XY: 30821 AN XY: 74374

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.434

Alfa AF: 0.511 Hom.: 8112

Bravo AF: 0.402

Asia WGS AF: 0.284 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.5
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12682293; hg19: chr8-29884077;