rs12488556

Variant names:

• chr3-26458718-G-A
• rs12488556

Your query was ambiguous. Multiple possible variants found:

• chr3-26458718-G-A
• chr3-26458718-G-C
• chr3-26458718-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 0.326 in 151,868 control chromosomes in the GnomAD database, including 8,480 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 0.33 (8480 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 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: 0.326 AC: 49502 AN: 151750 Hom.: 8454 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.326 AC: 49566 AN: 151868 Hom.: 8480 Cov.: 32 AF XY: 0.329 AC XY: 24411 AN XY: 74184

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.340

Alfa AF: 0.312 Hom.: 3459

Bravo AF: 0.327

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.8
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12488556; hg19: chr3-26500209;