rs12826786

Positions:

• chr12-53961717-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;