rs826917

Positions:

• chr12-130083017-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 0.212 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;