rs12893484

Variant names:

• chr14-53948020-G-A
• rs12893484

Your query was ambiguous. Multiple possible variants found:

• chr14-53948020-G-A
• chr14-53948020-G-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 0.43 in 151,836 control chromosomes in the GnomAD database, including 15,969 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 0.43 (15969 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 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: 0.431 AC: 65320 AN: 151718 Hom.: 15962 Cov.: 30

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.430 AC: 65342 AN: 151836 Hom.: 15969 Cov.: 30 AF XY: 0.428 AC XY: 31756 AN XY: 74184

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.429

Alfa AF: 0.502 Hom.: 8348

Bravo AF: 0.403

Asia WGS AF: 0.278 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	17
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12893484; hg19: chr14-54414738; COSMIC: COSV55417150;