rs12876893

Variant names:

• chr13-30828694-G-A
• rs12876893

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 0.314 in 151,978 control chromosomes in the GnomAD database, including 8,530 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 0.31 (8530 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 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: 0.314 AC: 47672 AN: 151860 Hom.: 8529 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.314 AC: 47697 AN: 151978 Hom.: 8530 Cov.: 31 AF XY: 0.321 AC XY: 23866 AN XY: 74278

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.332

Alfa AF: 0.348 Hom.: 11444

Bravo AF: 0.309

Asia WGS AF: 0.496 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12876893; hg19: chr13-31402831;