rs12483428

Variant names:

• chr21-25561470-T-C
• rs12483428

Your query was ambiguous. Multiple possible variants found:

• chr21-25561470-T-C
• chr21-25561470-T-G

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 0.082 in 152,064 control chromosomes in the GnomAD database, including 1,291 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 0.082 (1291 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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: 0.0817 AC: 12411 AN: 151946 Hom.: 1275 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0474

Gnomad FIN AF: 0.00792

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.00127

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0820 AC: 12465 AN: 152064 Hom.: 1291 Cov.: 31 AF XY: 0.0814 AC XY: 6054 AN XY: 74362

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.000865

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.0472

Gnomad4 FIN AF: 0.00792

Gnomad4 NFE AF: 0.00127

Gnomad4 OTH AF: 0.0607

Alfa AF: 0.0227 Hom.: 54

Bravo AF: 0.0973

Asia WGS AF: 0.112 AC: 390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12483428; hg19: chr21-26933782;