rs12583882

Variant names:

• chr13-46999481-A-G
• rs12583882

Your query was ambiguous. Multiple possible variants found:

• chr13-46999481-A-G
• chr13-46999481-A-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 0.268 in 152,120 control chromosomes in the GnomAD database, including 6,602 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 0.27 (6602 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 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: 0.268 AC: 40771 AN: 152002 Hom.: 6591 Cov.: 32

Gnomad AFR AF: 0.0822

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.268 AC: 40792 AN: 152120 Hom.: 6602 Cov.: 32 AF XY: 0.274 AC XY: 20384 AN XY: 74332

Gnomad4 AFR AF: 0.0820

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.250

Alfa AF: 0.311 Hom.: 5641

Bravo AF: 0.252

Asia WGS AF: 0.366 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12583882; hg19: chr13-47573616;