rs12876893

Positions:

• chr13-30828694-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;