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. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.311 AC: 12869 AN: 41402

American (AMR) AF: 0.318 AC: 4848 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1019 AN: 3468

East Asian (EAS) AF: 0.664 AC: 3428 AN: 5160

South Asian (SAS) AF: 0.365 AC: 1757 AN: 4820

European-Finnish (FIN) AF: 0.351 AC: 3687 AN: 10502

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20941 AN: 67940

Other (OTH) AF: 0.340 AC: 716 AN: 2104

Alfa AF: 0.311 Hom.: 3870

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
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs12488556; hg19: chr3-26500209;