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. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.591 AC: 24468 AN: 41428

American (AMR) AF: 0.500 AC: 7637 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1911 AN: 3470

East Asian (EAS) AF: 0.482 AC: 2489 AN: 5160

South Asian (SAS) AF: 0.517 AC: 2494 AN: 4822

European-Finnish (FIN) AF: 0.635 AC: 6706 AN: 10566

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40328 AN: 67946

Other (OTH) AF: 0.580 AC: 1224 AN: 2112

Alfa AF: 0.582 Hom.: 99599

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
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs12589063; hg19: chr14-89437440;