rs12589063

Variant names:

• chr14-88971096-A-G
• rs12589063

Your query was ambiguous. Multiple possible variants found:

• chr14-88971096-A-G
• chr14-88971096-A-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 0.579 in 151,964 control chromosomes in the GnomAD database, including 25,611 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 0.58 (25611 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 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: 0.579 AC: 87886 AN: 151846 Hom.: 25575 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.579 AC: 87969 AN: 151964 Hom.: 25611 Cov.: 32 AF XY: 0.576 AC XY: 42798 AN XY: 74272

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.580

Alfa AF: 0.581 Hom.: 42267

Bravo AF: 0.568

Asia WGS AF: 0.544 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12589063; hg19: chr14-89437440;