rs12826786

Variant names:

• chr12-53961717-C-T
• rs12826786

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 0.375 in 152,038 control chromosomes in the GnomAD database, including 11,144 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 0.37 (11144 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 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: 0.375 AC: 56906 AN: 151920 Hom.: 11104 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.375 AC: 57004 AN: 152038 Hom.: 11144 Cov.: 32 AF XY: 0.368 AC XY: 27378 AN XY: 74318

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.378

Alfa AF: 0.382 Hom.: 1621

Bravo AF: 0.390

Asia WGS AF: 0.321 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.5
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12826786; hg19: chr12-54355501;