rs12893288

Variant names:

• chr14-47891810-C-T
• rs12893288

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 0.207 in 151,898 control chromosomes in the GnomAD database, including 3,927 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 (3927 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 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: 0.207 AC: 31471 AN: 151780 Hom.: 3917 Cov.: 33

Gnomad AFR AF: 0.0652

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.207 AC: 31498 AN: 151898 Hom.: 3927 Cov.: 33 AF XY: 0.216 AC XY: 16015 AN XY: 74186

Gnomad4 AFR AF: 0.0651

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.233

Alfa AF: 0.224 Hom.: 721

Bravo AF: 0.198

Asia WGS AF: 0.399 AC: 1379 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.7
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12893288; hg19: chr14-48361013;