rs12488556

chr3-26458718-G-Achr3-26458718-G-Cchr3-26458718-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;