rs826917

Variant names:

• chr12-130083017-A-G
• rs826917

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 0.212 in 152,224 control chromosomes in the GnomAD database, including 3,544 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 0.21 (3544 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.259 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: 0.212 AC: 32320 AN: 152104 Hom.: 3541 Cov.: 33

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.212 AC: 32347 AN: 152224 Hom.: 3544 Cov.: 33 AF XY: 0.212 AC XY: 15792 AN XY: 74436

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.0575

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.221

Alfa AF: 0.226 Hom.: 2064

Bravo AF: 0.211

Asia WGS AF: 0.175 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs826917; hg19: chr12-130567562;